{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "80c4f8bf",
   "metadata": {},
   "source": [
    "# Part 3 — Graph Initialization & Management\n",
    "\n",
    "*Last updated:* 2026-01-08\n",
    "\n",
    "This notebook shows how to **build and cache** an IDTrack graph snapshot for:\n",
    "- `homo_sapiens` (human)\n",
    "- `mus_musculus` (mouse)\n",
    "- `sus_scrofa` (pig)\n",
    "\n",
    "A graph build is the most expensive step. The good news:\n",
    "- you usually do it **once per organism + snapshot boundary + external YAML configuration**\n",
    "- the snapshot can be **multi-assembly** (human has overlapping GRCh38/GRCh37; mouse/pig are clean-handoff by release but legacy builds are supported)\n",
    "- then you reuse the cached graph for fast conversions\n",
    "\n",
    "**Learning objectives**\n",
    "- Build (or load) a graph snapshot for each organism.\n",
    "- Verify that the snapshot exists on disk.\n",
    "- Learn practical graph-management habits (reload vs rebuild, cache hygiene).\n",
    "\n",
    "> **Prerequisite:** run `02_prepare_new_external_yaml.ipynb` first (especially important for mouse and pig).\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c557f533",
   "metadata": {},
   "source": [
    "## 3.0 — What you should expect (time / disk)\n",
    "\n",
    "Graph building can take:\n",
    "- minutes to hours (depends on organism, enabled externals, and cache status)\n",
    "- multiple GB of disk for cached tables + the graph pickle\n",
    "\n",
    "Plan for this like you would plan for downloading a reference genome + annotation.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "7d8b4430",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Load notebook utilities (collapsible output magic for tutorials)\n",
    "%load_ext _notebook_utils"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "8312a066",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Local repository: /Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache\n"
     ]
    }
   ],
   "source": [
    "# 1) Setup\n",
    "from __future__ import annotations\n",
    "\n",
    "import os\n",
    "from pathlib import Path\n",
    "\n",
    "import idtrack\n",
    "\n",
    "LOCAL_REPOSITORY = Path(os.environ.get('IDTRACK_LOCAL_REPO', './idtrack_cache')).resolve()\n",
    "LOCAL_REPOSITORY.mkdir(parents=True, exist_ok=True)\n",
    "\n",
    "api = idtrack.API(local_repository=str(LOCAL_REPOSITORY))\n",
    "api.configure_logger()\n",
    "\n",
    "print('Local repository:', LOCAL_REPOSITORY)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ebfc85d3",
   "metadata": {},
   "source": [
    "## 3.0.1 — Sanity check: do your external YAML files exist?\n",
    "\n",
    "Human has a packaged default, but for mouse and pig you should have local `*_externals_modified.yml` files.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "a039edd6",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "OK                                                      homo_sapiens_externals_modified.yml\n",
      "OK                                                      mus_musculus_externals_modified.yml\n",
      "OK                                                      sus_scrofa_externals_modified.yml\n"
     ]
    }
   ],
   "source": [
    "# External YAML presence (created in Part 2)\n",
    "human_yaml = LOCAL_REPOSITORY / 'homo_sapiens_externals_modified.yml'\n",
    "mouse_yaml = LOCAL_REPOSITORY / 'mus_musculus_externals_modified.yml'\n",
    "pig_yaml = LOCAL_REPOSITORY / 'sus_scrofa_externals_modified.yml'\n",
    "\n",
    "HAS_HUMAN_YAML = human_yaml.exists()\n",
    "HAS_MOUSE_YAML = mouse_yaml.exists()\n",
    "HAS_PIG_YAML = pig_yaml.exists()\n",
    "\n",
    "print((\"OK\" if HAS_HUMAN_YAML else \"NOTE: missing (human can fall back to packaged default)\").ljust(55), human_yaml.name)\n",
    "print((\"OK\" if HAS_MOUSE_YAML else \"MISSING (create in Part 2 for mouse)\").ljust(55), mouse_yaml.name)\n",
    "print((\"OK\" if HAS_PIG_YAML else \"MISSING (create in Part 2 for pig)\").ljust(55), pig_yaml.name)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c8848d4e",
   "metadata": {},
   "source": [
    "If a file is missing:\n",
    "- go back to `02_prepare_new_external_yaml.ipynb`\n",
    "- generate the template and create the `_modified.yml` file\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fe65092a",
   "metadata": {},
   "source": [
    "## 3.1–3.3 — Build graph snapshots (one per organism)\n",
    "\n",
    "The canonical pattern is:\n",
    "\n",
    "1. resolve organism name\n",
    "2. pick snapshot release\n",
    "3. (optional) choose a primary genome assembly for output (defaults to the newest/highest-priority assembly for that organism)\n",
    "4. `api.build_graph(...)`\n",
    "5. inspect + reuse\n",
    "\n",
    "We do this for each organism below. If you only need one organism, run only that section.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "81d96570",
   "metadata": {},
   "source": [
    "### 3.1 — Human graph initialization (multi-assembly)\n",
    "\n",
    "By default, the human snapshot is built with GRCh38 as the primary assembly (assembly code `38`), while also including GRCh37 (`37`) and\n",
    "older archives when they exist within the snapshot window.\n",
    "\n",
    "This is what enables atlas-building workflows where different datasets were annotated with different genome builds, but you want one unified\n",
    "identifier space.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "17ea5d79",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2026-01-11 21:05:28 INFO:verify_organism: Ensembl Rest API query to get the organism names and associated releases.\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "('homo_sapiens', 115)"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "organism, latest_release = api.resolve_organism('human')\n",
    "SNAPSHOT_RELEASE = latest_release  # pin to a specific release if needed\n",
    "organism, SNAPSHOT_RELEASE\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "a3c031c8",
   "metadata": {},
   "outputs": [
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       "<details class=\"idtrack-collapse\">\n",
       "<summary>Click to show build logs</summary>\n",
       "<pre class=\"idtrack-collapse-content\">2026-01-11 21:05:39 INFO:database_manager: Using assembly-specific release range for homo_sapiens assembly 38: releases 76-115 (from config [76, None])\n",
       "2026-01-11 21:05:46 INFO:graph_maker: The graph is being constructed: /Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_homo_sapiens_min48_max115_narrow.pickle\n",
       "2026-01-11 21:05:46 INFO:graph_maker: Graph is being created: gene\n",
       "2026-01-11 21:05:48 INFO:database_manager: Using assembly-specific release range for homo_sapiens assembly 37: releases 55-115 (from config [55, None])\n",
       "2026-01-11 21:06:04 INFO:database_manager: Using assembly-specific release range for homo_sapiens assembly 36: releases 48-54 (from config [48, 54])\n",
       "2026-01-11 21:06:09 WARNING:graph_maker: Edge weights ignored due to duplicate entries: 2.\n",
       "2026-01-11 21:06:09 INFO:graph_maker: Edges between across different IDs and self loops are being added.\n",
       "2026-01-11 21:06:11 INFO:graph_maker: Edges between the same IDs are being added.\n",
       "2026-01-11 21:06:36 WARNING:graph_maker: Retired ID come alive again: 8.\n",
       "2026-01-11 21:06:36 INFO:graph_maker: Edges showing the retirement of IDs are being added.\n",
       "2026-01-11 21:06:43 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.\n",
       "2026-01-11 21:06:51 WARNING:graph_maker: Nodes are deleted due to Ensembl ID history mistake: 3.\n",
       "2026-01-11 21:06:51 INFO:graph_maker: Self-loops for latest release entries are being added.\n",
       "2026-01-11 21:06:53 INFO:graph_maker: Node attributes are being added.\n",
       "2026-01-11 21:06:54 INFO:graph_maker: Graph is being created: transcript\n",
       "2026-01-11 21:06:56 INFO:graph_maker: Edges between across different IDs and self loops are being added.\n",
       "2026-01-11 21:07:02 INFO:graph_maker: Edges between the same IDs are being added.\n",
       "2026-01-11 21:08:43 WARNING:graph_maker: Retired ID come alive again: 5.\n",
       "2026-01-11 21:08:43 INFO:graph_maker: Edges showing the retirement of IDs are being added.\n",
       "2026-01-11 21:09:16 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.\n",
       "2026-01-11 21:09:47 INFO:graph_maker: Self-loops for latest release entries are being added.\n",
       "2026-01-11 21:09:59 INFO:graph_maker: Node attributes are being added.\n",
       "2026-01-11 21:10:10 INFO:graph_maker: Graph is being created: translation\n",
       "2026-01-11 21:10:10 WARNING:graph_maker: Edge weights ignored due to duplicate entries: 4.\n",
       "2026-01-11 21:10:10 INFO:graph_maker: Edges between across different IDs and self loops are being added.\n",
       "2026-01-11 21:10:11 INFO:graph_maker: Edges between the same IDs are being added.\n",
       "2026-01-11 21:10:50 WARNING:graph_maker: Retired ID come alive again: 166.\n",
       "2026-01-11 21:10:50 INFO:graph_maker: Edges showing the retirement of IDs are being added.\n",
       "2026-01-11 21:11:07 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.\n",
       "2026-01-11 21:11:22 WARNING:graph_maker: Nodes are deleted due to Ensembl ID history mistake: 1.\n",
       "2026-01-11 21:11:22 INFO:graph_maker: Self-loops for latest release entries are being added.\n",
       "2026-01-11 21:11:27 INFO:graph_maker: Node attributes are being added.\n",
       "2026-01-11 21:11:31 WARNING:graph_maker: Intersecting Ensembl nodes: Nodes in &#x27;transcript&#x27; will be replaced by &#x27;translation&#x27;: &#x27;ENST00000515292.1&#x27;.\n",
       "2026-01-11 21:11:39 INFO:graph_maker: Establishing connection between different forms.\n",
       "2026-01-11 21:18:08 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for &#x27;gene&#x27;.\n",
       "2026-01-11 21:32:15 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for &#x27;transcript&#x27;.\n",
       "2026-01-11 21:45:25 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for &#x27;translation&#x27;.\n",
       "2026-01-11 21:57:42 INFO:graph_maker: Versionless Ensembl IDs are being connected.\n",
       "2026-01-11 21:57:44 INFO:graph_maker: Edges between versionless ID to version ID has been added for &#x27;gene&#x27;, assembly 36.\n",
       "2026-01-11 21:57:55 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens77_processed_versioninfo_gene`\n",
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       "2026-01-11 21:59:25 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens107_processed_versioninfo_gene`\n",
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       "2026-01-11 21:59:37 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens111_processed_versioninfo_gene`\n",
       "2026-01-11 21:59:37 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens111_processed_ids_gene`\n",
       "2026-01-11 21:59:40 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens112_processed_versioninfo_gene`\n",
       "2026-01-11 21:59:40 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens112_processed_ids_gene`\n",
       "2026-01-11 21:59:43 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens113_processed_versioninfo_gene`\n",
       "2026-01-11 21:59:43 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens113_processed_ids_gene`\n",
       "2026-01-11 21:59:46 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens114_processed_versioninfo_gene`\n",
       "2026-01-11 21:59:46 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens114_processed_ids_gene`\n",
       "2026-01-11 21:59:49 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens115_processed_versioninfo_gene`\n",
       "2026-01-11 21:59:49 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens115_processed_ids_gene`\n",
       "2026-01-11 21:59:51 INFO:graph_maker: Edges between versionless ID to version ID has been added for &#x27;gene&#x27;, assembly 37.\n",
       "2026-01-11 21:59:51 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens76_processed_ids_gene`\n",
       "2026-01-11 21:59:52 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens77_processed_ids_gene`\n",
       "2026-01-11 21:59:53 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens78_processed_ids_gene`\n",
       "2026-01-11 21:59:54 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens79_processed_ids_gene`\n",
       "2026-01-11 21:59:56 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens80_processed_ids_gene`\n",
       "2026-01-11 21:59:57 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens81_processed_ids_gene`\n",
       "2026-01-11 21:59:58 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens82_processed_ids_gene`\n",
       "2026-01-11 21:59:59 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens83_processed_ids_gene`\n",
       "2026-01-11 22:00:01 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens84_processed_ids_gene`\n",
       "2026-01-11 22:00:02 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens85_processed_ids_gene`\n",
       "2026-01-11 22:00:03 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens86_processed_ids_gene`\n",
       "2026-01-11 22:00:04 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens87_processed_ids_gene`\n",
       "2026-01-11 22:00:05 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens88_processed_ids_gene`\n",
       "2026-01-11 22:00:07 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens89_processed_ids_gene`\n",
       "2026-01-11 22:00:08 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens90_processed_ids_gene`\n",
       "2026-01-11 22:00:09 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens91_processed_ids_gene`\n",
       "2026-01-11 22:00:10 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens92_processed_ids_gene`\n",
       "2026-01-11 22:00:12 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens93_processed_ids_gene`\n",
       "2026-01-11 22:00:13 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens94_processed_ids_gene`\n",
       "2026-01-11 22:00:14 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens95_processed_ids_gene`\n",
       "2026-01-11 22:00:15 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens96_processed_ids_gene`\n",
       "2026-01-11 22:00:17 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens97_processed_ids_gene`\n",
       "2026-01-11 22:00:18 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens98_processed_ids_gene`\n",
       "2026-01-11 22:00:19 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens99_processed_ids_gene`\n",
       "2026-01-11 22:00:21 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens100_processed_ids_gene`\n",
       "2026-01-11 22:00:22 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens101_processed_ids_gene`\n",
       "2026-01-11 22:00:23 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens102_processed_ids_gene`\n",
       "2026-01-11 22:00:24 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens103_processed_ids_gene`\n",
       "2026-01-11 22:00:26 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens104_processed_ids_gene`\n",
       "2026-01-11 22:00:27 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens105_processed_ids_gene`\n",
       "2026-01-11 22:00:28 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens106_processed_ids_gene`\n",
       "2026-01-11 22:00:29 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens107_processed_ids_gene`\n",
       "2026-01-11 22:00:31 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens108_processed_ids_gene`\n",
       "2026-01-11 22:00:32 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens109_processed_ids_gene`\n",
       "2026-01-11 22:00:33 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens110_processed_ids_gene`\n",
       "2026-01-11 22:00:35 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens111_processed_ids_gene`\n",
       "2026-01-11 22:00:36 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens112_processed_ids_gene`\n",
       "2026-01-11 22:00:38 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens113_processed_ids_gene`\n",
       "2026-01-11 22:00:39 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens114_processed_ids_gene`\n",
       "2026-01-11 22:00:41 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens115_processed_ids_gene`\n",
       "2026-01-11 22:00:42 INFO:graph_maker: Edges between versionless ID to version ID has been added for &#x27;gene&#x27;, assembly 38.\n",
       "2026-01-11 22:00:42 INFO:graph_maker: Synonymous external nodes are being merged into one.\n",
       "2026-01-11 22:00:47 INFO:graph_maker: Number of removed nodes in the process of merging synonymous nodes: 13316\n",
       "2026-01-11 22:02:30 INFO:graph_maker: The graph is being exported as &#x27;/Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_homo_sapiens_min48_max115_narrow.pickle&#x27;.\n",
       "2026-01-11 22:04:59 INFO:the_graph: Cached properties being calculated: available_genome_assemblies\n",
       "2026-01-11 22:04:59 INFO:the_graph: Cached properties being calculated: combined_edges\n",
       "2026-01-11 22:07:33 INFO:the_graph: Cached properties being calculated: combined_edges_genes\n",
       "2026-01-11 22:08:28 INFO:the_graph: Cached properties being calculated: combined_edges_assembly_specific_genes</pre>\n",
       "</details>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%%collapse Click to show build logs\n",
    "# Included for tutorial purposes only.\n",
    "\n",
    "# Build (or load) the graph snapshot\n",
    "# - calculate_caches=True speeds up later queries (slower build, faster use).\n",
    "api.build_graph(organism_name=organism, snapshot_release=SNAPSHOT_RELEASE, calculate_caches=False)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "defa075f",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Organism: homo_sapiens\n",
      "Snapshot release: 115\n",
      "Main assembly: 38\n",
      "Assemblies in this graph: [36, 37, 38]\n",
      "Nodes: 3682041\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2026-01-11 22:08:48 INFO:the_graph: Cached properties being calculated: available_external_databases\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Edges: 8615426\n",
      "External DBs enabled (count): 27\n",
      "External DBs (first 20): ['CCDS', 'Clone_based_ensembl_gene', 'Clone_based_vega_gene', 'EntrezGene', 'HGNC Symbol', 'Havana gene', 'Havana transcript', 'Havana translation', 'NCBI gene', 'NCBI gene (formerly Entrezgene)', 'RFAM', 'RefSeq_mRNA', 'RefSeq_mRNA_predicted', 'RefSeq_ncRNA', 'RefSeq_ncRNA_predicted', 'RefSeq_peptide', 'RefSeq_peptide_predicted', 'UniProtKB Gene Name', 'Uniprot/SPTREMBL', 'Uniprot/SWISSPROT']\n"
     ]
    }
   ],
   "source": [
    "# Quick inspection\n",
    "g = api.track.graph\n",
    "print('Organism:', g.graph.get('organism'))\n",
    "print('Snapshot release:', g.graph.get('ensembl_release'))\n",
    "print('Main assembly:', g.graph.get('genome_assembly'))\n",
    "print('Assemblies in this graph:', sorted(api.list_genome_assemblies()))\n",
    "print('Nodes:', g.number_of_nodes())\n",
    "print('Edges:', g.number_of_edges())\n",
    "\n",
    "aed = sorted(getattr(g, 'available_external_databases', []))\n",
    "print('External DBs enabled (count):', len(aed))\n",
    "print('External DBs (first 20):', aed[:20])\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "ab4d624a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[PosixPath('/Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_homo_sapiens_min48_max115_narrow.pickle')]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Where is the graph file stored?\n",
    "sorted(LOCAL_REPOSITORY.glob('graph_homo_sapiens*.pickle'))[-5:]\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cd4a8418",
   "metadata": {},
   "source": [
    "### 3.2 — Mouse graph initialization (clean handoff)\n",
    "\n",
    "Mouse is a clean-handoff species (one maintained assembly per release: GRCm37 → GRCm38 → GRCm39). Older assemblies mainly matter for\n",
    "legacy datasets and archive releases; you typically do not have overlapping assemblies within the same release.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "a65d177c",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2026-01-11 22:44:22 INFO:verify_organism: Ensembl Rest API query to get the organism names and associated releases.\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "('mus_musculus', 115)"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "organism, latest_release = api.resolve_organism('mus musculus')\n",
    "SNAPSHOT_RELEASE = latest_release\n",
    "organism, SNAPSHOT_RELEASE\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "1636a3c4",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<details class=\"idtrack-collapse\">\n",
       "<summary>Click to show build logs</summary>\n",
       "<pre class=\"idtrack-collapse-content\">2026-01-11 22:44:34 INFO:database_manager: Using assembly-specific release range for mus_musculus assembly 39: releases 103-115 (from config [103, None])\n",
       "2026-01-11 22:44:36 INFO:graph_maker: The graph is being constructed: /Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_mus_musculus_min48_max115_narrow.pickle\n",
       "2026-01-11 22:44:36 INFO:graph_maker: Graph is being created: gene\n",
       "2026-01-11 22:44:38 INFO:database_manager: Using assembly-specific release range for mus_musculus assembly 38: releases 68-102 (from config [68, 102])\n",
       "2026-01-11 22:44:46 INFO:database_manager: Using assembly-specific release range for mus_musculus assembly 37: releases 48-67 (from config [48, 67])\n",
       "2026-01-11 22:44:58 INFO:graph_maker: Edges between across different IDs and self loops are being added.\n",
       "2026-01-11 22:45:01 INFO:graph_maker: Edges between the same IDs are being added.\n",
       "2026-01-11 22:45:21 WARNING:graph_maker: Retired ID come alive again: 2.\n",
       "2026-01-11 22:45:21 INFO:graph_maker: Edges showing the retirement of IDs are being added.\n",
       "2026-01-11 22:45:27 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.\n",
       "2026-01-11 22:45:33 INFO:graph_maker: Self-loops for latest release entries are being added.\n",
       "2026-01-11 22:45:35 INFO:graph_maker: Node attributes are being added.\n",
       "2026-01-11 22:45:36 INFO:graph_maker: Graph is being created: transcript\n",
       "2026-01-11 22:45:37 INFO:graph_maker: Edges between across different IDs and self loops are being added.\n",
       "2026-01-11 22:45:41 INFO:graph_maker: Edges between the same IDs are being added.\n",
       "2026-01-11 22:46:38 WARNING:graph_maker: Retired ID come alive again: 3.\n",
       "2026-01-11 22:46:38 INFO:graph_maker: Edges showing the retirement of IDs are being added.\n",
       "2026-01-11 22:46:56 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.\n",
       "2026-01-11 22:47:13 INFO:graph_maker: Self-loops for latest release entries are being added.\n",
       "2026-01-11 22:47:19 INFO:graph_maker: Node attributes are being added.\n",
       "2026-01-11 22:47:25 INFO:graph_maker: Graph is being created: translation\n",
       "2026-01-11 22:47:25 INFO:graph_maker: Edges between across different IDs and self loops are being added.\n",
       "2026-01-11 22:47:26 INFO:graph_maker: Edges between the same IDs are being added.\n",
       "2026-01-11 22:47:46 WARNING:graph_maker: Retired ID come alive again: 2.\n",
       "2026-01-11 22:47:46 INFO:graph_maker: Edges showing the retirement of IDs are being added.\n",
       "2026-01-11 22:47:56 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.\n",
       "2026-01-11 22:48:05 INFO:graph_maker: Self-loops for latest release entries are being added.\n",
       "2026-01-11 22:48:06 INFO:graph_maker: Node attributes are being added.\n",
       "2026-01-11 22:48:12 INFO:graph_maker: Establishing connection between different forms.\n",
       "2026-01-11 22:48:48 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens62_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:48:50 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens62_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:48:51 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens62_common_relationcurrent`\n",
       "2026-01-11 22:48:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens63_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:48:57 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens63_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:48:59 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens63_common_relationcurrent`\n",
       "2026-01-11 22:49:12 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens64_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:49:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens64_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:49:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens64_common_relationcurrent`\n",
       "2026-01-11 22:49:19 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens65_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:49:20 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens65_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:49:21 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens65_common_relationcurrent`\n",
       "2026-01-11 22:49:25 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens66_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:49:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens66_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:49:27 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens66_common_relationcurrent`\n",
       "2026-01-11 22:49:31 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens67_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:49:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens67_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:49:33 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens67_common_relationcurrent`\n",
       "2026-01-11 22:49:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens68_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:49:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens68_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:49:40 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens68_common_relationcurrent`\n",
       "2026-01-11 22:49:45 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens69_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:49:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens69_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:49:47 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens69_common_relationcurrent`\n",
       "2026-01-11 22:49:51 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens70_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:49:52 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens70_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:49:53 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens70_common_relationcurrent`\n",
       "2026-01-11 22:49:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens71_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:49:57 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens71_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:49:59 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens71_common_relationcurrent`\n",
       "2026-01-11 22:50:02 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens72_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:50:03 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens72_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:50:05 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens72_common_relationcurrent`\n",
       "2026-01-11 22:50:08 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens73_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:50:09 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens73_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:50:10 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens73_common_relationcurrent`\n",
       "2026-01-11 22:50:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens74_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:50:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens74_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:50:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens74_common_relationcurrent`\n",
       "2026-01-11 22:50:20 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens75_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:50:21 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens75_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:50:22 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens75_common_relationcurrent`\n",
       "2026-01-11 22:50:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens76_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:50:27 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens76_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:50:28 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens76_common_relationcurrent`\n",
       "2026-01-11 22:50:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens77_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:50:33 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens77_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:50:34 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens77_common_relationcurrent`\n",
       "2026-01-11 22:50:38 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens78_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:50:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens78_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:50:40 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens78_common_relationcurrent`\n",
       "2026-01-11 22:50:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens79_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:50:47 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens79_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:50:48 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens79_common_relationcurrent`\n",
       "2026-01-11 22:50:52 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens80_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:50:54 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens80_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:50:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens80_common_relationcurrent`\n",
       "2026-01-11 22:50:59 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens81_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:51:01 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens81_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:51:02 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens81_common_relationcurrent`\n",
       "2026-01-11 22:51:08 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens82_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:51:10 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens82_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:51:11 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens82_common_relationcurrent`\n",
       "2026-01-11 22:51:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens83_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:51:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens83_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:51:19 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens83_common_relationcurrent`\n",
       "2026-01-11 22:51:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens84_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:51:25 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens84_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:51:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens84_common_relationcurrent`\n",
       "2026-01-11 22:51:31 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens85_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:51:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens85_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:51:34 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens85_common_relationcurrent`\n",
       "2026-01-11 22:51:38 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens86_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:51:40 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens86_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:51:41 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens86_common_relationcurrent`\n",
       "2026-01-11 22:51:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens87_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:51:47 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens87_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:51:49 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens87_common_relationcurrent`\n",
       "2026-01-11 22:51:54 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens88_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:51:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens88_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:51:57 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens88_common_relationcurrent`\n",
       "2026-01-11 22:52:02 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens89_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:52:04 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens89_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:52:05 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens89_common_relationcurrent`\n",
       "2026-01-11 22:52:10 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens90_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:52:12 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens90_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:52:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens90_common_relationcurrent`\n",
       "2026-01-11 22:52:19 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens91_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:52:21 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens91_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:52:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens91_common_relationcurrent`\n",
       "2026-01-11 22:52:28 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens92_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:52:30 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens92_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:52:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens92_common_relationcurrent`\n",
       "2026-01-11 22:52:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens93_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:52:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens93_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:52:41 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens93_common_relationcurrent`\n",
       "2026-01-11 22:52:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens94_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:52:48 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens94_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:52:50 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens94_common_relationcurrent`\n",
       "2026-01-11 22:52:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens95_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:52:57 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens95_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:52:59 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens95_common_relationcurrent`\n",
       "2026-01-11 22:53:05 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens96_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:53:07 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens96_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:53:08 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens96_common_relationcurrent`\n",
       "2026-01-11 22:53:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens97_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:53:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens97_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:53:18 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens97_common_relationcurrent`\n",
       "2026-01-11 22:53:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens98_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:53:28 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens98_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:53:29 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens98_common_relationcurrent`\n",
       "2026-01-11 22:53:35 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens99_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:53:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens99_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:53:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens99_common_relationcurrent`\n",
       "2026-01-11 22:53:45 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens100_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:53:47 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens100_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:53:48 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens100_common_relationcurrent`\n",
       "2026-01-11 22:53:54 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens101_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:53:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens101_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:53:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens101_common_relationcurrent`\n",
       "2026-01-11 22:54:04 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens102_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:54:06 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens102_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:54:07 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens102_common_relationcurrent`\n",
       "2026-01-11 22:54:13 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens103_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:54:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens103_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:54:18 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens103_common_relationcurrent`\n",
       "2026-01-11 22:54:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens104_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:54:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens104_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:54:28 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens104_common_relationcurrent`\n",
       "2026-01-11 22:54:33 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens105_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:54:36 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens105_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:54:38 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens105_common_relationcurrent`\n",
       "2026-01-11 22:54:44 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens106_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:54:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens106_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:54:48 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens106_common_relationcurrent`\n",
       "2026-01-11 22:54:54 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens107_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:54:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens107_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:54:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens107_common_relationcurrent`\n",
       "2026-01-11 22:55:05 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens108_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:55:07 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens108_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:55:09 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens108_common_relationcurrent`\n",
       "2026-01-11 22:55:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens109_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:55:18 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens109_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:55:20 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens109_common_relationcurrent`\n",
       "2026-01-11 22:55:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens110_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:55:29 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens110_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:55:31 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens110_common_relationcurrent`\n",
       "2026-01-11 22:55:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens111_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:55:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens111_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:55:41 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens111_common_relationcurrent`\n",
       "2026-01-11 22:55:47 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens112_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:55:50 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens112_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:55:52 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens112_common_relationcurrent`\n",
       "2026-01-11 22:55:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens113_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:56:02 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens113_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:56:05 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens113_common_relationcurrent`\n",
       "2026-01-11 22:56:18 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens114_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:56:22 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens114_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:56:25 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens114_common_relationcurrent`\n",
       "2026-01-11 22:56:36 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens115_processed_idsraw_transcript_gene`\n",
       "2026-01-11 22:56:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens115_processed_idsraw_translation_gene`\n",
       "2026-01-11 22:56:42 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens115_common_relationcurrent`\n",
       "2026-01-11 22:56:52 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for &#x27;gene&#x27;.\n",
       "2026-01-11 22:56:56 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 52.\n",
       "2026-01-11 22:56:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens52_processed_external_relevant_gene`\n",
       "2026-01-11 22:57:06 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens53_processed_external_relevant_gene`\n",
       "2026-01-11 22:57:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens54_processed_external_relevant_gene`\n",
       "2026-01-11 22:57:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens55_processed_external_relevant_gene`\n",
       "2026-01-11 22:57:27 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens56_processed_external_relevant_gene`\n",
       "2026-01-11 22:57:33 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens57_processed_external_relevant_gene`\n",
       "2026-01-11 22:57:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens58_processed_external_relevant_gene`\n",
       "2026-01-11 22:57:45 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens59_processed_external_relevant_gene`\n",
       "2026-01-11 22:57:52 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens60_processed_external_relevant_gene`\n",
       "2026-01-11 22:57:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens61_processed_external_relevant_gene`\n",
       "2026-01-11 22:58:05 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens62_processed_external_relevant_gene`\n",
       "2026-01-11 22:58:13 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens63_processed_external_relevant_gene`\n",
       "2026-01-11 22:58:27 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens64_processed_external_relevant_gene`\n",
       "2026-01-11 22:58:41 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens65_processed_external_relevant_gene`\n",
       "2026-01-11 22:59:00 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens66_processed_external_relevant_gene`\n",
       "2026-01-11 22:59:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens67_processed_external_relevant_gene`\n",
       "2026-01-11 22:59:27 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens68_processed_external_relevant_gene`\n",
       "2026-01-11 22:59:41 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens69_processed_external_relevant_gene`\n",
       "2026-01-11 22:59:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens70_processed_external_relevant_gene`\n",
       "2026-01-11 23:00:09 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens71_processed_external_relevant_gene`\n",
       "2026-01-11 23:00:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens72_processed_external_relevant_gene`\n",
       "2026-01-11 23:00:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens73_processed_external_relevant_gene`\n",
       "2026-01-11 23:00:52 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens74_processed_external_relevant_gene`\n",
       "2026-01-11 23:01:07 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens75_processed_external_relevant_gene`\n",
       "2026-01-11 23:01:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens76_processed_external_relevant_gene`\n",
       "2026-01-11 23:01:42 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens77_processed_external_relevant_gene`\n",
       "2026-01-11 23:02:02 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens78_processed_external_relevant_gene`\n",
       "2026-01-11 23:02:22 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens79_processed_external_relevant_gene`\n",
       "2026-01-11 23:02:42 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens80_processed_external_relevant_gene`\n",
       "2026-01-11 23:03:11 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens81_processed_external_relevant_gene`\n",
       "2026-01-11 23:03:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens82_processed_external_relevant_gene`\n",
       "2026-01-11 23:03:54 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens83_processed_external_relevant_gene`\n",
       "2026-01-11 23:04:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens84_processed_external_relevant_gene`\n",
       "2026-01-11 23:04:36 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens85_processed_external_relevant_gene`\n",
       "2026-01-11 23:04:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens86_processed_external_relevant_gene`\n",
       "2026-01-11 23:05:18 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens87_processed_external_relevant_gene`\n",
       "2026-01-11 23:05:41 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens88_processed_external_relevant_gene`\n",
       "2026-01-11 23:05:59 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens89_processed_external_relevant_gene`\n",
       "2026-01-11 23:06:12 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens90_processed_external_relevant_gene`\n",
       "2026-01-11 23:06:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens91_processed_external_relevant_gene`\n",
       "2026-01-11 23:06:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens92_processed_external_relevant_gene`\n",
       "2026-01-11 23:06:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens93_processed_external_relevant_gene`\n",
       "2026-01-11 23:07:11 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens94_processed_external_relevant_gene`\n",
       "2026-01-11 23:07:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens95_processed_external_relevant_gene`\n",
       "2026-01-11 23:07:36 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens96_processed_external_relevant_gene`\n",
       "2026-01-11 23:07:49 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens97_processed_external_relevant_gene`\n",
       "2026-01-11 23:08:02 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens98_processed_external_relevant_gene`\n",
       "2026-01-11 23:08:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens99_processed_external_relevant_gene`\n",
       "2026-01-11 23:08:31 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens100_processed_external_relevant_gene`\n",
       "2026-01-11 23:08:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens101_processed_external_relevant_gene`\n",
       "2026-01-11 23:09:21 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens102_processed_external_relevant_gene`\n",
       "2026-01-11 23:09:42 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens103_processed_external_relevant_gene`\n",
       "2026-01-11 23:10:08 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens104_processed_external_relevant_gene`\n",
       "2026-01-11 23:10:22 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens105_processed_external_relevant_gene`\n",
       "2026-01-11 23:10:35 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens106_processed_external_relevant_gene`\n",
       "2026-01-11 23:10:49 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens107_processed_external_relevant_gene`\n",
       "2026-01-11 23:11:02 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens108_processed_external_relevant_gene`\n",
       "2026-01-11 23:11:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens109_processed_external_relevant_gene`\n",
       "2026-01-11 23:11:30 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens110_processed_external_relevant_gene`\n",
       "2026-01-11 23:11:44 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens111_processed_external_relevant_gene`\n",
       "2026-01-11 23:11:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens112_processed_external_relevant_gene`\n",
       "2026-01-11 23:12:12 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens113_processed_external_relevant_gene`\n",
       "2026-01-11 23:12:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens114_processed_external_relevant_gene`\n",
       "2026-01-11 23:12:40 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens115_processed_external_relevant_gene`\n",
       "2026-01-11 23:12:48 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for &#x27;transcript&#x27;.\n",
       "2026-01-11 23:12:52 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 50.\n",
       "2026-01-11 23:12:57 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens50_processed_external_relevant_transcript`\n",
       "2026-01-11 23:13:00 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 51.\n",
       "2026-01-11 23:13:06 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens51_processed_external_relevant_transcript`\n",
       "2026-01-11 23:13:09 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 52.\n",
       "2026-01-11 23:13:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens52_processed_external_relevant_transcript`\n",
       "2026-01-11 23:13:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens53_processed_external_relevant_transcript`\n",
       "2026-01-11 23:13:51 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens54_processed_external_relevant_transcript`\n",
       "2026-01-11 23:14:09 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens55_processed_external_relevant_transcript`\n",
       "2026-01-11 23:14:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens56_processed_external_relevant_transcript`\n",
       "2026-01-11 23:14:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens57_processed_external_relevant_transcript`\n",
       "2026-01-11 23:14:33 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens58_processed_external_relevant_transcript`\n",
       "2026-01-11 23:14:44 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens59_processed_external_relevant_transcript`\n",
       "2026-01-11 23:14:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens60_processed_external_relevant_transcript`\n",
       "2026-01-11 23:15:06 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens61_processed_external_relevant_transcript`\n",
       "2026-01-11 23:15:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens62_processed_external_relevant_transcript`\n",
       "2026-01-11 23:15:28 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens63_processed_external_relevant_transcript`\n",
       "2026-01-11 23:15:40 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens64_processed_external_relevant_transcript`\n",
       "2026-01-11 23:15:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens65_processed_external_relevant_transcript`\n",
       "2026-01-11 23:16:09 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens66_processed_external_relevant_transcript`\n",
       "2026-01-11 23:16:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens67_processed_external_relevant_transcript`\n",
       "2026-01-11 23:16:36 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens68_processed_external_relevant_transcript`\n",
       "2026-01-11 23:16:50 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens69_processed_external_relevant_transcript`\n",
       "2026-01-11 23:17:04 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens70_processed_external_relevant_transcript`\n",
       "2026-01-11 23:17:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens71_processed_external_relevant_transcript`\n",
       "2026-01-11 23:17:31 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens72_processed_external_relevant_transcript`\n",
       "2026-01-11 23:17:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens73_processed_external_relevant_transcript`\n",
       "2026-01-11 23:18:00 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens74_processed_external_relevant_transcript`\n",
       "2026-01-11 23:18:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens75_processed_external_relevant_transcript`\n",
       "2026-01-11 23:18:31 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens76_processed_external_relevant_transcript`\n",
       "2026-01-11 23:18:49 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens77_processed_external_relevant_transcript`\n",
       "2026-01-11 23:19:07 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens78_processed_external_relevant_transcript`\n",
       "2026-01-11 23:19:25 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens79_processed_external_relevant_transcript`\n",
       "2026-01-11 23:19:43 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens80_processed_external_relevant_transcript`\n",
       "2026-01-11 23:20:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens81_processed_external_relevant_transcript`\n",
       "2026-01-11 23:20:36 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens82_processed_external_relevant_transcript`\n",
       "2026-01-11 23:20:54 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens83_processed_external_relevant_transcript`\n",
       "2026-01-11 23:21:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens84_processed_external_relevant_transcript`\n",
       "2026-01-11 23:21:33 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens85_processed_external_relevant_transcript`\n",
       "2026-01-11 23:21:53 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens86_processed_external_relevant_transcript`\n",
       "2026-01-11 23:22:13 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens87_processed_external_relevant_transcript`\n",
       "2026-01-11 23:22:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens88_processed_external_relevant_transcript`\n",
       "2026-01-11 23:22:52 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens89_processed_external_relevant_transcript`\n",
       "2026-01-11 23:23:08 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens90_processed_external_relevant_transcript`\n",
       "2026-01-11 23:23:29 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens91_processed_external_relevant_transcript`\n",
       "2026-01-11 23:23:51 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens92_processed_external_relevant_transcript`\n",
       "2026-01-11 23:24:08 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens93_processed_external_relevant_transcript`\n",
       "2026-01-11 23:24:25 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens94_processed_external_relevant_transcript`\n",
       "2026-01-11 23:24:42 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens95_processed_external_relevant_transcript`\n",
       "2026-01-11 23:24:59 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens96_processed_external_relevant_transcript`\n",
       "2026-01-11 23:25:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens97_processed_external_relevant_transcript`\n",
       "2026-01-11 23:25:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens98_processed_external_relevant_transcript`\n",
       "2026-01-11 23:25:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens99_processed_external_relevant_transcript`\n",
       "2026-01-11 23:26:20 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens100_processed_external_relevant_transcript`\n",
       "2026-01-11 23:26:50 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens101_processed_external_relevant_transcript`\n",
       "2026-01-11 23:27:19 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens102_processed_external_relevant_transcript`\n",
       "2026-01-11 23:27:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens103_processed_external_relevant_transcript`\n",
       "2026-01-11 23:27:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens104_processed_external_relevant_transcript`\n",
       "2026-01-11 23:28:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens105_processed_external_relevant_transcript`\n",
       "2026-01-11 23:28:34 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens106_processed_external_relevant_transcript`\n",
       "2026-01-11 23:28:53 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens107_processed_external_relevant_transcript`\n",
       "2026-01-11 23:29:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens108_processed_external_relevant_transcript`\n",
       "2026-01-11 23:29:35 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens109_processed_external_relevant_transcript`\n",
       "2026-01-11 23:29:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens110_processed_external_relevant_transcript`\n",
       "2026-01-11 23:30:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens111_processed_external_relevant_transcript`\n",
       "2026-01-11 23:30:36 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens112_processed_external_relevant_transcript`\n",
       "2026-01-11 23:30:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens113_processed_external_relevant_transcript`\n",
       "2026-01-11 23:31:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens114_processed_external_relevant_transcript`\n",
       "2026-01-11 23:31:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens115_processed_external_relevant_transcript`\n",
       "2026-01-11 23:31:47 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for &#x27;translation&#x27;.\n",
       "2026-01-11 23:31:50 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 48.\n",
       "2026-01-11 23:31:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens48_processed_external_relevant_translation`\n",
       "2026-01-11 23:32:09 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 49.\n",
       "2026-01-11 23:32:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens49_processed_external_relevant_translation`\n",
       "2026-01-11 23:32:25 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 50.\n",
       "2026-01-11 23:32:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens50_processed_external_relevant_translation`\n",
       "2026-01-11 23:32:40 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 51.\n",
       "2026-01-11 23:32:47 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens51_processed_external_relevant_translation`\n",
       "2026-01-11 23:32:54 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 52.\n",
       "2026-01-11 23:33:01 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens52_processed_external_relevant_translation`\n",
       "2026-01-11 23:33:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens53_processed_external_relevant_translation`\n",
       "2026-01-11 23:33:33 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens54_processed_external_relevant_translation`\n",
       "2026-01-11 23:33:50 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens55_processed_external_relevant_translation`\n",
       "2026-01-11 23:34:04 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens56_processed_external_relevant_translation`\n",
       "2026-01-11 23:34:21 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens57_processed_external_relevant_translation`\n",
       "2026-01-11 23:35:06 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens58_processed_external_relevant_translation`\n",
       "2026-01-11 23:35:25 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens59_processed_external_relevant_translation`\n",
       "2026-01-11 23:35:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens60_processed_external_relevant_translation`\n",
       "2026-01-11 23:36:05 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens61_processed_external_relevant_translation`\n",
       "2026-01-11 23:36:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens62_processed_external_relevant_translation`\n",
       "2026-01-11 23:36:40 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens63_processed_external_relevant_translation`\n",
       "2026-01-11 23:36:57 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens64_processed_external_relevant_translation`\n",
       "2026-01-11 23:37:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens65_processed_external_relevant_translation`\n",
       "2026-01-11 23:37:35 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens66_processed_external_relevant_translation`\n",
       "2026-01-11 23:37:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens67_processed_external_relevant_translation`\n",
       "2026-01-11 23:38:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens68_processed_external_relevant_translation`\n",
       "2026-01-11 23:38:34 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens69_processed_external_relevant_translation`\n",
       "2026-01-11 23:38:53 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens70_processed_external_relevant_translation`\n",
       "2026-01-11 23:39:11 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens71_processed_external_relevant_translation`\n",
       "2026-01-11 23:39:28 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens72_processed_external_relevant_translation`\n",
       "2026-01-11 23:39:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens73_processed_external_relevant_translation`\n",
       "2026-01-11 23:40:04 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens74_processed_external_relevant_translation`\n",
       "2026-01-11 23:40:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens75_processed_external_relevant_translation`\n",
       "2026-01-11 23:40:44 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens76_processed_external_relevant_translation`\n",
       "2026-01-11 23:41:10 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens77_processed_external_relevant_translation`\n",
       "2026-01-11 23:41:34 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens78_processed_external_relevant_translation`\n",
       "2026-01-11 23:41:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens79_processed_external_relevant_translation`\n",
       "2026-01-11 23:42:22 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens80_processed_external_relevant_translation`\n",
       "2026-01-11 23:42:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens81_processed_external_relevant_translation`\n",
       "2026-01-11 23:43:11 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens82_processed_external_relevant_translation`\n",
       "2026-01-11 23:43:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens83_processed_external_relevant_translation`\n",
       "2026-01-11 23:43:57 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens84_processed_external_relevant_translation`\n",
       "2026-01-11 23:44:19 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens85_processed_external_relevant_translation`\n",
       "2026-01-11 23:44:42 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens86_processed_external_relevant_translation`\n",
       "2026-01-11 23:45:06 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens87_processed_external_relevant_translation`\n",
       "2026-01-11 23:45:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens88_processed_external_relevant_translation`\n",
       "2026-01-11 23:45:50 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens89_processed_external_relevant_translation`\n",
       "2026-01-11 23:46:05 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens90_processed_external_relevant_translation`\n",
       "2026-01-11 23:46:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens91_processed_external_relevant_translation`\n",
       "2026-01-11 23:46:42 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens92_processed_external_relevant_translation`\n",
       "2026-01-11 23:46:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens93_processed_external_relevant_translation`\n",
       "2026-01-11 23:47:13 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens94_processed_external_relevant_translation`\n",
       "2026-01-11 23:47:28 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens95_processed_external_relevant_translation`\n",
       "2026-01-11 23:47:43 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens96_processed_external_relevant_translation`\n",
       "2026-01-11 23:47:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens97_processed_external_relevant_translation`\n",
       "2026-01-11 23:48:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens98_processed_external_relevant_translation`\n",
       "2026-01-11 23:48:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens99_processed_external_relevant_translation`\n",
       "2026-01-11 23:48:52 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens100_processed_external_relevant_translation`\n",
       "2026-01-11 23:49:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens101_processed_external_relevant_translation`\n",
       "2026-01-11 23:49:38 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens102_processed_external_relevant_translation`\n",
       "2026-01-11 23:49:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens103_processed_external_relevant_translation`\n",
       "2026-01-11 23:50:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens104_processed_external_relevant_translation`\n",
       "2026-01-11 23:50:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens105_processed_external_relevant_translation`\n",
       "2026-01-11 23:50:45 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens106_processed_external_relevant_translation`\n",
       "2026-01-11 23:51:00 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens107_processed_external_relevant_translation`\n",
       "2026-01-11 23:51:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens108_processed_external_relevant_translation`\n",
       "2026-01-11 23:51:29 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens109_processed_external_relevant_translation`\n",
       "2026-01-11 23:51:45 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens110_processed_external_relevant_translation`\n",
       "2026-01-11 23:52:01 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens111_processed_external_relevant_translation`\n",
       "2026-01-11 23:52:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens112_processed_external_relevant_translation`\n",
       "2026-01-11 23:52:31 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens113_processed_external_relevant_translation`\n",
       "2026-01-11 23:52:47 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens114_processed_external_relevant_translation`\n",
       "2026-01-11 23:53:03 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens115_processed_external_relevant_translation`\n",
       "2026-01-11 23:53:10 INFO:graph_maker: Versionless Ensembl IDs are being connected.\n",
       "2026-01-11 23:53:10 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens48_processed_ids_gene`\n",
       "2026-01-11 23:53:11 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens49_processed_ids_gene`\n",
       "2026-01-11 23:53:11 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens50_processed_ids_gene`\n",
       "2026-01-11 23:53:12 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens51_processed_ids_gene`\n",
       "2026-01-11 23:53:12 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens52_processed_ids_gene`\n",
       "2026-01-11 23:53:13 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens53_processed_ids_gene`\n",
       "2026-01-11 23:53:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens54_processed_ids_gene`\n",
       "2026-01-11 23:53:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens55_processed_ids_gene`\n",
       "2026-01-11 23:53:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens56_processed_ids_gene`\n",
       "2026-01-11 23:53:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens57_processed_ids_gene`\n",
       "2026-01-11 23:53:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens58_processed_ids_gene`\n",
       "2026-01-11 23:53:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens59_processed_ids_gene`\n",
       "2026-01-11 23:53:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens60_processed_ids_gene`\n",
       "2026-01-11 23:53:18 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens61_processed_ids_gene`\n",
       "2026-01-11 23:53:18 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens62_processed_ids_gene`\n",
       "2026-01-11 23:53:19 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens63_processed_ids_gene`\n",
       "2026-01-11 23:53:20 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens64_processed_ids_gene`\n",
       "2026-01-11 23:53:20 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens65_processed_ids_gene`\n",
       "2026-01-11 23:53:21 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens66_processed_ids_gene`\n",
       "2026-01-11 23:53:21 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens67_processed_ids_gene`\n",
       "2026-01-11 23:53:22 INFO:graph_maker: Edges between versionless ID to version ID has been added for &#x27;gene&#x27;, assembly 37.\n",
       "2026-01-11 23:53:22 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens68_processed_ids_gene`\n",
       "2026-01-11 23:53:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens69_processed_ids_gene`\n",
       "2026-01-11 23:53:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens70_processed_ids_gene`\n",
       "2026-01-11 23:53:24 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens71_processed_ids_gene`\n",
       "2026-01-11 23:53:25 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens72_processed_ids_gene`\n",
       "2026-01-11 23:53:25 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens73_processed_ids_gene`\n",
       "2026-01-11 23:53:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens74_processed_ids_gene`\n",
       "2026-01-11 23:53:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens75_processed_ids_gene`\n",
       "2026-01-11 23:53:27 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens76_processed_ids_gene`\n",
       "2026-01-11 23:53:28 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens77_processed_ids_gene`\n",
       "2026-01-11 23:53:29 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens78_processed_ids_gene`\n",
       "2026-01-11 23:53:29 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens79_processed_ids_gene`\n",
       "2026-01-11 23:53:30 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens80_processed_ids_gene`\n",
       "2026-01-11 23:53:31 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens81_processed_ids_gene`\n",
       "2026-01-11 23:53:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens82_processed_ids_gene`\n",
       "2026-01-11 23:53:33 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens83_processed_ids_gene`\n",
       "2026-01-11 23:53:34 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens84_processed_ids_gene`\n",
       "2026-01-11 23:53:35 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens85_processed_ids_gene`\n",
       "2026-01-11 23:53:35 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens86_processed_ids_gene`\n",
       "2026-01-11 23:53:36 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens87_processed_ids_gene`\n",
       "2026-01-11 23:53:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens88_processed_ids_gene`\n",
       "2026-01-11 23:53:38 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens89_processed_ids_gene`\n",
       "2026-01-11 23:53:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens90_processed_ids_gene`\n",
       "2026-01-11 23:53:40 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens91_processed_ids_gene`\n",
       "2026-01-11 23:53:41 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens92_processed_ids_gene`\n",
       "2026-01-11 23:53:42 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens93_processed_ids_gene`\n",
       "2026-01-11 23:53:43 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens94_processed_ids_gene`\n",
       "2026-01-11 23:53:44 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens95_processed_ids_gene`\n",
       "2026-01-11 23:53:45 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens96_processed_ids_gene`\n",
       "2026-01-11 23:53:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens97_processed_ids_gene`\n",
       "2026-01-11 23:53:47 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens98_processed_ids_gene`\n",
       "2026-01-11 23:53:48 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens99_processed_ids_gene`\n",
       "2026-01-11 23:53:49 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens100_processed_ids_gene`\n",
       "2026-01-11 23:53:50 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens101_processed_ids_gene`\n",
       "2026-01-11 23:53:51 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens102_processed_ids_gene`\n",
       "2026-01-11 23:53:52 INFO:graph_maker: Edges between versionless ID to version ID has been added for &#x27;gene&#x27;, assembly 38.\n",
       "2026-01-11 23:53:52 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens103_processed_ids_gene`\n",
       "2026-01-11 23:53:54 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens104_processed_ids_gene`\n",
       "2026-01-11 23:53:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens105_processed_ids_gene`\n",
       "2026-01-11 23:53:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens106_processed_ids_gene`\n",
       "2026-01-11 23:53:57 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens107_processed_ids_gene`\n",
       "2026-01-11 23:53:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens108_processed_ids_gene`\n",
       "2026-01-11 23:53:59 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens109_processed_ids_gene`\n",
       "2026-01-11 23:54:00 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens110_processed_ids_gene`\n",
       "2026-01-11 23:54:02 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens111_processed_ids_gene`\n",
       "2026-01-11 23:54:03 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens112_processed_ids_gene`\n",
       "2026-01-11 23:54:04 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens113_processed_ids_gene`\n",
       "2026-01-11 23:54:06 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens114_processed_ids_gene`\n",
       "2026-01-11 23:54:07 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens115_processed_ids_gene`\n",
       "2026-01-11 23:54:09 INFO:graph_maker: Edges between versionless ID to version ID has been added for &#x27;gene&#x27;, assembly 39.\n",
       "2026-01-11 23:54:09 INFO:graph_maker: Synonymous external nodes are being merged into one.\n",
       "2026-01-11 23:54:52 INFO:graph_maker: Number of removed nodes in the process of merging synonymous nodes: 38082\n",
       "2026-01-11 23:55:12 INFO:graph_maker: The graph is being exported as &#x27;/Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_mus_musculus_min48_max115_narrow.pickle&#x27;.\n",
       "2026-01-11 23:56:06 INFO:the_graph: Cached properties being calculated: available_genome_assemblies\n",
       "2026-01-11 23:56:06 INFO:the_graph: Cached properties being calculated: combined_edges\n",
       "2026-01-11 23:57:03 INFO:the_graph: Cached properties being calculated: combined_edges_genes\n",
       "2026-01-11 23:58:12 INFO:the_graph: Cached properties being calculated: combined_edges_assembly_specific_genes</pre>\n",
       "</details>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%%collapse Click to show build logs\n",
    "# Included for tutorial purposes only.\n",
    "\n",
    "# Build (or load) the mouse graph snapshot\n",
    "if HAS_MOUSE_YAML:\n",
    "    api.build_graph(organism_name=organism, snapshot_release=SNAPSHOT_RELEASE, calculate_caches=False)\n",
    "else:\n",
    "    print('Skipping mouse build: mus_musculus_externals_modified.yml is missing (run Part 2 first).')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "41ff577b",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Organism: mus_musculus\n",
      "Snapshot release: 115\n",
      "Main assembly: 39\n",
      "Assemblies in this graph: [37, 38, 39]\n",
      "Nodes: 2476278\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2026-01-11 23:58:19 INFO:the_graph: Cached properties being calculated: available_external_databases\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Edges: 5367328\n",
      "External DBs enabled (count): 28\n",
      "External DBs (first 20): ['CCDS', 'Clone_based_ensembl_gene', 'Clone_based_vega_gene', 'EntrezGene', 'Havana gene', 'Havana transcript', 'Havana translation', 'MGI Symbol', 'NCBI gene', 'NCBI gene (formerly Entrezgene)', 'RFAM', 'RefSeq_mRNA', 'RefSeq_mRNA_predicted', 'RefSeq_ncRNA', 'RefSeq_ncRNA_predicted', 'RefSeq_peptide', 'RefSeq_peptide_predicted', 'UniProtKB Gene Name', 'Uniprot/SPTREMBL', 'Uniprot/SWISSPROT']\n"
     ]
    }
   ],
   "source": [
    "if HAS_MOUSE_YAML:\n",
    "    g = api.track.graph\n",
    "    print('Organism:', g.graph.get('organism'))\n",
    "    print('Snapshot release:', g.graph.get('ensembl_release'))\n",
    "    print('Main assembly:', g.graph.get('genome_assembly'))\n",
    "    print('Assemblies in this graph:', sorted(api.list_genome_assemblies()))\n",
    "    print('Nodes:', g.number_of_nodes())\n",
    "    print('Edges:', g.number_of_edges())\n",
    "\n",
    "    aed = sorted(getattr(g, 'available_external_databases', []))\n",
    "    print('External DBs enabled (count):', len(aed))\n",
    "    print('External DBs (first 20):', aed[:20])\n",
    "else:\n",
    "    print('Mouse graph not built (missing YAML).')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "4372ac04",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[PosixPath('/Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_mus_musculus_min48_max115_narrow.pickle')]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sorted(LOCAL_REPOSITORY.glob('graph_mus_musculus*.pickle'))[-5:]\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b854f51e",
   "metadata": {},
   "source": [
    "### 3.3 — Pig graph initialization (clean handoff)\n",
    "\n",
    "Pig is a clean-handoff species (one maintained assembly per release: Sscrofa9.2 → Sscrofa10.2 → Sscrofa11.1). Older assemblies mainly\n",
    "matter for legacy datasets and archive releases; you typically do not have overlapping assemblies within the same release.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "3f8bd787",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2026-01-11 23:58:21 INFO:verify_organism: Ensembl Rest API query to get the organism names and associated releases.\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "('sus_scrofa', 115)"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "organism, latest_release = api.resolve_organism('sus scrofa')\n",
    "SNAPSHOT_RELEASE = latest_release\n",
    "organism, SNAPSHOT_RELEASE\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "56dd4c1e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<details class=\"idtrack-collapse\">\n",
       "<summary>Click to show build logs</summary>\n",
       "<pre class=\"idtrack-collapse-content\">2026-01-11 23:58:41 INFO:database_manager: Using assembly-specific release range for sus_scrofa assembly 111: releases 90-115 (from config [90, None])\n",
       "2026-01-11 23:58:46 INFO:graph_maker: The graph is being constructed: /Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_sus_scrofa_min48_max115_narrow.pickle\n",
       "2026-01-11 23:58:46 INFO:graph_maker: Graph is being created: gene\n",
       "2026-01-11 23:58:47 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_versioninfo_gene`\n",
       "2026-01-11 23:58:49 INFO:database_manager: Using assembly-specific release range for sus_scrofa assembly 102: releases 67-89 (from config [67, 89])\n",
       "2026-01-11 23:58:54 INFO:database_manager: Using assembly-specific release range for sus_scrofa assembly 9: releases 56-66 (from config [56, 66])\n",
       "2026-01-11 23:59:07 INFO:database_manager: Raw table for `stable_id_event` on ensembl release `115` was downloaded.\n",
       "2026-01-11 23:59:07 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_mysql_stable_id_event`\n",
       "2026-01-11 23:59:20 INFO:database_manager: Raw table for `mapping_session` on ensembl release `115` was downloaded.\n",
       "2026-01-11 23:59:20 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_mysql_mapping_session`\n",
       "2026-01-11 23:59:21 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_idhistory_narrow_gene`\n",
       "2026-01-11 23:59:24 INFO:graph_maker: Edges between across different IDs and self loops are being added.\n",
       "2026-01-11 23:59:25 INFO:graph_maker: Edges between the same IDs are being added.\n",
       "2026-01-11 23:59:31 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_versioninfo_gene`\n",
       "2026-01-11 23:59:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_versioninfo_gene`\n",
       "2026-01-11 23:59:35 INFO:graph_maker: Edges showing the retirement of IDs are being added.\n",
       "2026-01-11 23:59:39 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.\n",
       "2026-01-11 23:59:43 INFO:graph_maker: Self-loops for latest release entries are being added.\n",
       "2026-01-11 23:59:44 INFO:graph_maker: Node attributes are being added.\n",
       "2026-01-11 23:59:45 INFO:graph_maker: Graph is being created: transcript\n",
       "2026-01-11 23:59:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_versioninfo_transcript`\n",
       "2026-01-11 23:59:48 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_idhistory_narrow_transcript`\n",
       "2026-01-11 23:59:52 INFO:graph_maker: Edges between across different IDs and self loops are being added.\n",
       "2026-01-11 23:59:53 INFO:graph_maker: Edges between the same IDs are being added.\n",
       "2026-01-12 00:00:04 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_versioninfo_transcript`\n",
       "2026-01-12 00:00:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_versioninfo_transcript`\n",
       "2026-01-12 00:00:10 INFO:graph_maker: Edges showing the retirement of IDs are being added.\n",
       "2026-01-12 00:00:16 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.\n",
       "2026-01-12 00:00:22 INFO:graph_maker: Self-loops for latest release entries are being added.\n",
       "2026-01-12 00:00:23 INFO:graph_maker: Node attributes are being added.\n",
       "2026-01-12 00:00:25 INFO:graph_maker: Graph is being created: translation\n",
       "2026-01-12 00:00:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_versioninfo_translation`\n",
       "2026-01-12 00:00:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_idhistory_narrow_translation`\n",
       "2026-01-12 00:00:32 INFO:graph_maker: Edges between across different IDs and self loops are being added.\n",
       "2026-01-12 00:00:34 INFO:graph_maker: Edges between the same IDs are being added.\n",
       "2026-01-12 00:00:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_versioninfo_translation`\n",
       "2026-01-12 00:00:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_versioninfo_translation`\n",
       "2026-01-12 00:00:47 INFO:graph_maker: Edges showing the retirement of IDs are being added.\n",
       "2026-01-12 00:00:52 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.\n",
       "2026-01-12 00:00:57 INFO:graph_maker: Self-loops for latest release entries are being added.\n",
       "2026-01-12 00:00:58 INFO:graph_maker: Node attributes are being added.\n",
       "2026-01-12 00:01:01 INFO:graph_maker: Establishing connection between different forms.\n",
       "2026-01-12 00:01:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens56_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:01:03 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens56_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:01:03 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens56_common_relationcurrent`\n",
       "2026-01-12 00:01:05 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens57_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:01:06 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens57_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:01:06 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens57_common_relationcurrent`\n",
       "2026-01-12 00:01:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens58_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:01:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens58_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:01:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens58_common_relationcurrent`\n",
       "2026-01-12 00:01:11 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens59_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:01:12 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens59_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:01:12 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens59_common_relationcurrent`\n",
       "2026-01-12 00:01:14 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens60_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:01:15 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens60_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:01:15 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens60_common_relationcurrent`\n",
       "2026-01-12 00:01:17 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens61_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:01:18 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens61_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:01:18 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens61_common_relationcurrent`\n",
       "2026-01-12 00:01:20 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens62_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:01:21 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens62_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:01:21 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens62_common_relationcurrent`\n",
       "2026-01-12 00:01:23 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens63_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:01:24 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens63_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:01:24 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens63_common_relationcurrent`\n",
       "2026-01-12 00:01:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens64_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:01:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens64_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:01:39 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens64_common_relationcurrent`\n",
       "2026-01-12 00:01:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens65_processed_idsraw_transcript_gene`\n",
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       "2026-01-12 00:01:41 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_idsraw_transcript_gene`\n",
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       "2026-01-12 00:01:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_common_relationcurrent`\n",
       "2026-01-12 00:01:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens67_processed_idsraw_transcript_gene`\n",
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       "2026-01-12 00:02:35 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens86_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:02:36 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens86_common_relationcurrent`\n",
       "2026-01-12 00:02:37 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens87_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:02:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens87_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:02:39 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens87_common_relationcurrent`\n",
       "2026-01-12 00:02:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens88_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:02:41 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens88_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:02:41 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens88_common_relationcurrent`\n",
       "2026-01-12 00:02:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:02:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:02:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_common_relationcurrent`\n",
       "2026-01-12 00:02:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens90_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:02:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens90_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:02:47 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens90_common_relationcurrent`\n",
       "2026-01-12 00:02:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens91_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:02:50 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens91_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:02:51 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens91_common_relationcurrent`\n",
       "2026-01-12 00:02:53 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens92_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:02:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens92_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:02:55 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens92_common_relationcurrent`\n",
       "2026-01-12 00:02:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens93_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:02:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens93_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:02:59 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens93_common_relationcurrent`\n",
       "2026-01-12 00:03:01 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens94_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:03:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens94_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:03:03 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens94_common_relationcurrent`\n",
       "2026-01-12 00:03:05 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens95_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:03:06 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens95_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:03:07 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens95_common_relationcurrent`\n",
       "2026-01-12 00:03:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens96_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:03:10 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens96_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:03:11 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens96_common_relationcurrent`\n",
       "2026-01-12 00:03:13 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens97_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:03:14 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens97_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:03:15 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens97_common_relationcurrent`\n",
       "2026-01-12 00:03:17 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens98_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:03:18 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens98_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:03:19 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens98_common_relationcurrent`\n",
       "2026-01-12 00:03:22 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens99_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:03:23 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens99_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:03:24 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens99_common_relationcurrent`\n",
       "2026-01-12 00:03:27 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens100_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:03:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens100_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:03:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens100_common_relationcurrent`\n",
       "2026-01-12 00:03:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens101_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:03:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens101_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:03:35 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens101_common_relationcurrent`\n",
       "2026-01-12 00:03:37 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens102_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:03:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens102_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:03:39 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens102_common_relationcurrent`\n",
       "2026-01-12 00:03:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens103_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:03:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens103_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:03:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens103_common_relationcurrent`\n",
       "2026-01-12 00:03:47 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens104_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:03:48 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens104_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:03:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens104_common_relationcurrent`\n",
       "2026-01-12 00:03:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens105_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:03:53 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens105_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:03:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens105_common_relationcurrent`\n",
       "2026-01-12 00:03:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens106_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:03:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens106_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:03:59 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens106_common_relationcurrent`\n",
       "2026-01-12 00:04:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens107_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:04:03 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens107_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:04:04 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens107_common_relationcurrent`\n",
       "2026-01-12 00:04:07 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens108_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:04:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens108_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:04:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens108_common_relationcurrent`\n",
       "2026-01-12 00:04:12 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens109_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:04:13 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens109_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:04:14 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens109_common_relationcurrent`\n",
       "2026-01-12 00:04:17 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens110_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:04:18 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens110_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:04:20 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens110_common_relationcurrent`\n",
       "2026-01-12 00:04:22 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens111_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:04:23 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens111_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:04:25 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens111_common_relationcurrent`\n",
       "2026-01-12 00:04:27 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens112_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:04:29 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens112_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:04:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens112_common_relationcurrent`\n",
       "2026-01-12 00:04:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens113_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:04:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens113_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:04:35 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens113_common_relationcurrent`\n",
       "2026-01-12 00:04:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens114_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:04:39 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens114_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:04:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens114_common_relationcurrent`\n",
       "2026-01-12 00:04:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_idsraw_transcript_gene`\n",
       "2026-01-12 00:04:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_idsraw_translation_gene`\n",
       "2026-01-12 00:04:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_common_relationcurrent`\n",
       "2026-01-12 00:04:48 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for &#x27;gene&#x27;.\n",
       "2026-01-12 00:04:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens61_processed_external_relevant_gene`\n",
       "2026-01-12 00:04:51 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens62_processed_external_relevant_gene`\n",
       "2026-01-12 00:04:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens63_processed_external_relevant_gene`\n",
       "2026-01-12 00:04:55 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens64_processed_external_relevant_gene`\n",
       "2026-01-12 00:04:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens65_processed_external_relevant_gene`\n",
       "2026-01-12 00:05:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_external_relevant_gene`\n",
       "2026-01-12 00:05:07 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens67_processed_external_relevant_gene`\n",
       "2026-01-12 00:05:11 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens68_processed_external_relevant_gene`\n",
       "2026-01-12 00:05:16 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens69_processed_external_relevant_gene`\n",
       "2026-01-12 00:05:23 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens70_processed_external_relevant_gene`\n",
       "2026-01-12 00:05:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens71_processed_external_relevant_gene`\n",
       "2026-01-12 00:05:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens72_processed_external_relevant_gene`\n",
       "2026-01-12 00:05:37 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens73_processed_external_relevant_gene`\n",
       "2026-01-12 00:05:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens74_processed_external_relevant_gene`\n",
       "2026-01-12 00:05:48 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens75_processed_external_relevant_gene`\n",
       "2026-01-12 00:05:53 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens76_processed_external_relevant_gene`\n",
       "2026-01-12 00:05:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens77_processed_external_relevant_gene`\n",
       "2026-01-12 00:06:04 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens78_processed_external_relevant_gene`\n",
       "2026-01-12 00:06:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens79_processed_external_relevant_gene`\n",
       "2026-01-12 00:06:14 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens80_processed_external_relevant_gene`\n",
       "2026-01-12 00:06:19 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens81_processed_external_relevant_gene`\n",
       "2026-01-12 00:06:25 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens82_processed_external_relevant_gene`\n",
       "2026-01-12 00:06:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens83_processed_external_relevant_gene`\n",
       "2026-01-12 00:06:36 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens84_processed_external_relevant_gene`\n",
       "2026-01-12 00:06:41 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens85_processed_external_relevant_gene`\n",
       "2026-01-12 00:06:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens86_processed_external_relevant_gene`\n",
       "2026-01-12 00:06:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens87_processed_external_relevant_gene`\n",
       "2026-01-12 00:06:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens88_processed_external_relevant_gene`\n",
       "2026-01-12 00:07:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_external_relevant_gene`\n",
       "2026-01-12 00:07:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens90_processed_external_relevant_gene`\n",
       "2026-01-12 00:07:11 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens90_processed_external_relevant_gene`\n",
       "2026-01-12 00:07:19 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens91_processed_external_relevant_gene`\n",
       "2026-01-12 00:07:22 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens91_processed_external_relevant_gene`\n",
       "2026-01-12 00:07:29 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens92_processed_external_relevant_gene`\n",
       "2026-01-12 00:07:33 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens92_processed_external_relevant_gene`\n",
       "2026-01-12 00:07:41 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens93_processed_external_relevant_gene`\n",
       "2026-01-12 00:07:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens93_processed_external_relevant_gene`\n",
       "2026-01-12 00:07:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens94_processed_external_relevant_gene`\n",
       "2026-01-12 00:07:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens94_processed_external_relevant_gene`\n",
       "2026-01-12 00:08:06 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens95_processed_external_relevant_gene`\n",
       "2026-01-12 00:08:10 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens95_processed_external_relevant_gene`\n",
       "2026-01-12 00:08:19 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens96_processed_external_relevant_gene`\n",
       "2026-01-12 00:08:22 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens96_processed_external_relevant_gene`\n",
       "2026-01-12 00:08:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens97_processed_external_relevant_gene`\n",
       "2026-01-12 00:08:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens97_processed_external_relevant_gene`\n",
       "2026-01-12 00:08:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens98_processed_external_relevant_gene`\n",
       "2026-01-12 00:08:47 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens98_processed_external_relevant_gene`\n",
       "2026-01-12 00:08:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens99_processed_external_relevant_gene`\n",
       "2026-01-12 00:09:01 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens99_processed_external_relevant_gene`\n",
       "2026-01-12 00:09:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens100_processed_external_relevant_gene`\n",
       "2026-01-12 00:09:16 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens101_processed_external_relevant_gene`\n",
       "2026-01-12 00:09:23 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens102_processed_external_relevant_gene`\n",
       "2026-01-12 00:09:29 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens103_processed_external_relevant_gene`\n",
       "2026-01-12 00:09:36 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens104_processed_external_relevant_gene`\n",
       "2026-01-12 00:09:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens105_processed_external_relevant_gene`\n",
       "2026-01-12 00:09:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens106_processed_external_relevant_gene`\n",
       "2026-01-12 00:09:56 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens107_processed_external_relevant_gene`\n",
       "2026-01-12 00:10:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens108_processed_external_relevant_gene`\n",
       "2026-01-12 00:10:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens109_processed_external_relevant_gene`\n",
       "2026-01-12 00:10:15 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens110_processed_external_relevant_gene`\n",
       "2026-01-12 00:10:23 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens111_processed_external_relevant_gene`\n",
       "2026-01-12 00:10:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens112_processed_external_relevant_gene`\n",
       "2026-01-12 00:10:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens113_processed_external_relevant_gene`\n",
       "2026-01-12 00:10:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens114_processed_external_relevant_gene`\n",
       "2026-01-12 00:10:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_external_relevant_gene`\n",
       "2026-01-12 00:10:55 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for &#x27;transcript&#x27;.\n",
       "2026-01-12 00:10:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens64_processed_external_relevant_transcript`\n",
       "2026-01-12 00:10:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens65_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:00 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens67_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:03 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens68_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:06 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens69_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens70_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:11 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens71_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:13 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens72_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:16 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens73_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:18 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens74_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:21 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens75_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:23 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens76_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens77_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens78_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens79_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:35 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens80_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:37 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens81_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens82_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens83_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:48 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens84_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:51 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens85_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens86_processed_external_relevant_transcript`\n",
       "2026-01-12 00:11:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens87_processed_external_relevant_transcript`\n",
       "2026-01-12 00:12:00 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens88_processed_external_relevant_transcript`\n",
       "2026-01-12 00:12:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_external_relevant_transcript`\n",
       "2026-01-12 00:13:01 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens90_processed_external_relevant_transcript`\n",
       "2026-01-12 00:13:03 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens90_processed_external_relevant_transcript`\n",
       "2026-01-12 00:13:07 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens91_processed_external_relevant_transcript`\n",
       "2026-01-12 00:13:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens91_processed_external_relevant_transcript`\n",
       "2026-01-12 00:13:14 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens92_processed_external_relevant_transcript`\n",
       "2026-01-12 00:13:17 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens92_processed_external_relevant_transcript`\n",
       "2026-01-12 00:13:22 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens93_processed_external_relevant_transcript`\n",
       "2026-01-12 00:13:25 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens93_processed_external_relevant_transcript`\n",
       "2026-01-12 00:13:31 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens94_processed_external_relevant_transcript`\n",
       "2026-01-12 00:13:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens94_processed_external_relevant_transcript`\n",
       "2026-01-12 00:13:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens95_processed_external_relevant_transcript`\n",
       "2026-01-12 00:13:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens95_processed_external_relevant_transcript`\n",
       "2026-01-12 00:13:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens96_processed_external_relevant_transcript`\n",
       "2026-01-12 00:13:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens96_processed_external_relevant_transcript`\n",
       "2026-01-12 00:13:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens97_processed_external_relevant_transcript`\n",
       "2026-01-12 00:14:01 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens97_processed_external_relevant_transcript`\n",
       "2026-01-12 00:14:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens98_processed_external_relevant_transcript`\n",
       "2026-01-12 00:14:11 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens98_processed_external_relevant_transcript`\n",
       "2026-01-12 00:14:18 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens99_processed_external_relevant_transcript`\n",
       "2026-01-12 00:14:21 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens99_processed_external_relevant_transcript`\n",
       "2026-01-12 00:14:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens100_processed_external_relevant_transcript`\n",
       "2026-01-12 00:14:35 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens101_processed_external_relevant_transcript`\n",
       "2026-01-12 00:14:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens102_processed_external_relevant_transcript`\n",
       "2026-01-12 00:14:48 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens103_processed_external_relevant_transcript`\n",
       "2026-01-12 00:14:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens104_processed_external_relevant_transcript`\n",
       "2026-01-12 00:15:01 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens105_processed_external_relevant_transcript`\n",
       "2026-01-12 00:15:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens106_processed_external_relevant_transcript`\n",
       "2026-01-12 00:15:15 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens107_processed_external_relevant_transcript`\n",
       "2026-01-12 00:15:22 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens108_processed_external_relevant_transcript`\n",
       "2026-01-12 00:15:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens109_processed_external_relevant_transcript`\n",
       "2026-01-12 00:15:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens110_processed_external_relevant_transcript`\n",
       "2026-01-12 00:15:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens111_processed_external_relevant_transcript`\n",
       "2026-01-12 00:15:53 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens112_processed_external_relevant_transcript`\n",
       "2026-01-12 00:16:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens113_processed_external_relevant_transcript`\n",
       "2026-01-12 00:16:10 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens114_processed_external_relevant_transcript`\n",
       "2026-01-12 00:16:19 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_external_relevant_transcript`\n",
       "2026-01-12 00:16:21 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for &#x27;translation&#x27;.\n",
       "2026-01-12 00:16:22 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens56_processed_external_relevant_translation`\n",
       "2026-01-12 00:16:24 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens57_processed_external_relevant_translation`\n",
       "2026-01-12 00:16:25 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens58_processed_external_relevant_translation`\n",
       "2026-01-12 00:16:27 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens59_processed_external_relevant_translation`\n",
       "2026-01-12 00:16:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens60_processed_external_relevant_translation`\n",
       "2026-01-12 00:16:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens61_processed_external_relevant_translation`\n",
       "2026-01-12 00:16:31 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens62_processed_external_relevant_translation`\n",
       "2026-01-12 00:16:33 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens63_processed_external_relevant_translation`\n",
       "2026-01-12 00:16:36 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens64_processed_external_relevant_translation`\n",
       "2026-01-12 00:16:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens65_processed_external_relevant_translation`\n",
       "2026-01-12 00:16:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_external_relevant_translation`\n",
       "2026-01-12 00:16:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens67_processed_external_relevant_translation`\n",
       "2026-01-12 00:16:53 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens68_processed_external_relevant_translation`\n",
       "2026-01-12 00:16:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens69_processed_external_relevant_translation`\n",
       "2026-01-12 00:17:04 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens70_processed_external_relevant_translation`\n",
       "2026-01-12 00:17:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens71_processed_external_relevant_translation`\n",
       "2026-01-12 00:17:15 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens72_processed_external_relevant_translation`\n",
       "2026-01-12 00:17:21 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens73_processed_external_relevant_translation`\n",
       "2026-01-12 00:17:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens74_processed_external_relevant_translation`\n",
       "2026-01-12 00:17:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens75_processed_external_relevant_translation`\n",
       "2026-01-12 00:17:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens76_processed_external_relevant_translation`\n",
       "2026-01-12 00:17:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens77_processed_external_relevant_translation`\n",
       "2026-01-12 00:17:50 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens78_processed_external_relevant_translation`\n",
       "2026-01-12 00:17:56 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens79_processed_external_relevant_translation`\n",
       "2026-01-12 00:18:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens80_processed_external_relevant_translation`\n",
       "2026-01-12 00:18:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens81_processed_external_relevant_translation`\n",
       "2026-01-12 00:18:14 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens82_processed_external_relevant_translation`\n",
       "2026-01-12 00:18:21 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens83_processed_external_relevant_translation`\n",
       "2026-01-12 00:18:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens84_processed_external_relevant_translation`\n",
       "2026-01-12 00:18:31 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens85_processed_external_relevant_translation`\n",
       "2026-01-12 00:18:37 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens86_processed_external_relevant_translation`\n",
       "2026-01-12 00:18:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens87_processed_external_relevant_translation`\n",
       "2026-01-12 00:18:47 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens88_processed_external_relevant_translation`\n",
       "2026-01-12 00:18:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_external_relevant_translation`\n",
       "2026-01-12 00:18:56 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens90_processed_external_relevant_translation`\n",
       "2026-01-12 00:19:01 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens90_processed_external_relevant_translation`\n",
       "2026-01-12 00:19:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens91_processed_external_relevant_translation`\n",
       "2026-01-12 00:19:13 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens91_processed_external_relevant_translation`\n",
       "2026-01-12 00:19:20 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens92_processed_external_relevant_translation`\n",
       "2026-01-12 00:19:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens92_processed_external_relevant_translation`\n",
       "2026-01-12 00:19:33 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens93_processed_external_relevant_translation`\n",
       "2026-01-12 00:19:39 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens93_processed_external_relevant_translation`\n",
       "2026-01-12 00:19:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens94_processed_external_relevant_translation`\n",
       "2026-01-12 00:19:51 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens94_processed_external_relevant_translation`\n",
       "2026-01-12 00:20:01 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens95_processed_external_relevant_translation`\n",
       "2026-01-12 00:20:06 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens95_processed_external_relevant_translation`\n",
       "2026-01-12 00:20:14 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens96_processed_external_relevant_translation`\n",
       "2026-01-12 00:20:19 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens96_processed_external_relevant_translation`\n",
       "2026-01-12 00:20:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens97_processed_external_relevant_translation`\n",
       "2026-01-12 00:20:31 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens97_processed_external_relevant_translation`\n",
       "2026-01-12 00:20:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens98_processed_external_relevant_translation`\n",
       "2026-01-12 00:20:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens98_processed_external_relevant_translation`\n",
       "2026-01-12 00:20:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens99_processed_external_relevant_translation`\n",
       "2026-01-12 00:20:59 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens99_processed_external_relevant_translation`\n",
       "2026-01-12 00:21:07 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens100_processed_external_relevant_translation`\n",
       "2026-01-12 00:21:16 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens101_processed_external_relevant_translation`\n",
       "2026-01-12 00:21:25 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens102_processed_external_relevant_translation`\n",
       "2026-01-12 00:21:33 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens103_processed_external_relevant_translation`\n",
       "2026-01-12 00:21:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens104_processed_external_relevant_translation`\n",
       "2026-01-12 00:21:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens105_processed_external_relevant_translation`\n",
       "2026-01-12 00:22:03 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens106_processed_external_relevant_translation`\n",
       "2026-01-12 00:22:10 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens107_processed_external_relevant_translation`\n",
       "2026-01-12 00:22:19 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens108_processed_external_relevant_translation`\n",
       "2026-01-12 00:22:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens109_processed_external_relevant_translation`\n",
       "2026-01-12 00:22:36 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens110_processed_external_relevant_translation`\n",
       "2026-01-12 00:22:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens111_processed_external_relevant_translation`\n",
       "2026-01-12 00:22:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens112_processed_external_relevant_translation`\n",
       "2026-01-12 00:23:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens113_processed_external_relevant_translation`\n",
       "2026-01-12 00:23:11 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens114_processed_external_relevant_translation`\n",
       "2026-01-12 00:23:20 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_external_relevant_translation`\n",
       "2026-01-12 00:23:25 INFO:graph_maker: Versionless Ensembl IDs are being connected.\n",
       "2026-01-12 00:23:25 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens56_processed_ids_gene`\n",
       "2026-01-12 00:23:25 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens57_processed_ids_gene`\n",
       "2026-01-12 00:23:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens58_processed_ids_gene`\n",
       "2026-01-12 00:23:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens59_processed_ids_gene`\n",
       "2026-01-12 00:23:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens60_processed_ids_gene`\n",
       "2026-01-12 00:23:27 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens61_processed_ids_gene`\n",
       "2026-01-12 00:23:27 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens62_processed_ids_gene`\n",
       "2026-01-12 00:23:27 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens63_processed_ids_gene`\n",
       "2026-01-12 00:23:27 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens64_processed_ids_gene`\n",
       "2026-01-12 00:23:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens65_processed_ids_gene`\n",
       "2026-01-12 00:23:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_ids_gene`\n",
       "2026-01-12 00:23:28 INFO:graph_maker: Edges between versionless ID to version ID has been added for &#x27;gene&#x27;, assembly 9.\n",
       "2026-01-12 00:23:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens67_processed_ids_gene`\n",
       "2026-01-12 00:23:29 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens68_processed_ids_gene`\n",
       "2026-01-12 00:23:29 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens69_processed_ids_gene`\n",
       "2026-01-12 00:23:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens70_processed_ids_gene`\n",
       "2026-01-12 00:23:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens71_processed_ids_gene`\n",
       "2026-01-12 00:23:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens72_processed_ids_gene`\n",
       "2026-01-12 00:23:31 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens73_processed_ids_gene`\n",
       "2026-01-12 00:23:31 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens74_processed_ids_gene`\n",
       "2026-01-12 00:23:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens75_processed_ids_gene`\n",
       "2026-01-12 00:23:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens76_processed_ids_gene`\n",
       "2026-01-12 00:23:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens77_processed_ids_gene`\n",
       "2026-01-12 00:23:33 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens78_processed_ids_gene`\n",
       "2026-01-12 00:23:33 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens79_processed_ids_gene`\n",
       "2026-01-12 00:23:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens80_processed_ids_gene`\n",
       "2026-01-12 00:23:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens81_processed_ids_gene`\n",
       "2026-01-12 00:23:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens82_processed_ids_gene`\n",
       "2026-01-12 00:23:35 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens83_processed_ids_gene`\n",
       "2026-01-12 00:23:35 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens84_processed_ids_gene`\n",
       "2026-01-12 00:23:36 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens85_processed_ids_gene`\n",
       "2026-01-12 00:23:36 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens86_processed_ids_gene`\n",
       "2026-01-12 00:23:37 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens87_processed_ids_gene`\n",
       "2026-01-12 00:23:37 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens88_processed_ids_gene`\n",
       "2026-01-12 00:23:37 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_ids_gene`\n",
       "2026-01-12 00:23:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens90_processed_versioninfo_gene`\n",
       "2026-01-12 00:23:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens90_processed_ids_gene`\n",
       "2026-01-12 00:23:39 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens91_processed_versioninfo_gene`\n",
       "2026-01-12 00:23:39 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens91_processed_ids_gene`\n",
       "2026-01-12 00:23:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens92_processed_versioninfo_gene`\n",
       "2026-01-12 00:23:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens92_processed_ids_gene`\n",
       "2026-01-12 00:23:41 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens93_processed_versioninfo_gene`\n",
       "2026-01-12 00:23:41 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens93_processed_ids_gene`\n",
       "2026-01-12 00:23:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens94_processed_versioninfo_gene`\n",
       "2026-01-12 00:23:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens94_processed_ids_gene`\n",
       "2026-01-12 00:23:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens95_processed_versioninfo_gene`\n",
       "2026-01-12 00:23:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens95_processed_ids_gene`\n",
       "2026-01-12 00:23:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens96_processed_versioninfo_gene`\n",
       "2026-01-12 00:23:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens96_processed_ids_gene`\n",
       "2026-01-12 00:23:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens97_processed_versioninfo_gene`\n",
       "2026-01-12 00:23:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens97_processed_ids_gene`\n",
       "2026-01-12 00:23:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens98_processed_versioninfo_gene`\n",
       "2026-01-12 00:23:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens98_processed_ids_gene`\n",
       "2026-01-12 00:23:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens99_processed_versioninfo_gene`\n",
       "2026-01-12 00:23:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens99_processed_ids_gene`\n",
       "2026-01-12 00:23:46 INFO:graph_maker: Edges between versionless ID to version ID has been added for &#x27;gene&#x27;, assembly 102.\n",
       "2026-01-12 00:23:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens90_processed_ids_gene`\n",
       "2026-01-12 00:23:47 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens91_processed_ids_gene`\n",
       "2026-01-12 00:23:47 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens92_processed_ids_gene`\n",
       "2026-01-12 00:23:48 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens93_processed_ids_gene`\n",
       "2026-01-12 00:23:48 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens94_processed_ids_gene`\n",
       "2026-01-12 00:23:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens95_processed_ids_gene`\n",
       "2026-01-12 00:23:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens96_processed_ids_gene`\n",
       "2026-01-12 00:23:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens97_processed_ids_gene`\n",
       "2026-01-12 00:23:50 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens98_processed_ids_gene`\n",
       "2026-01-12 00:23:51 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens99_processed_ids_gene`\n",
       "2026-01-12 00:23:51 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens100_processed_ids_gene`\n",
       "2026-01-12 00:23:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens101_processed_ids_gene`\n",
       "2026-01-12 00:23:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens102_processed_ids_gene`\n",
       "2026-01-12 00:23:53 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens103_processed_ids_gene`\n",
       "2026-01-12 00:23:53 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens104_processed_ids_gene`\n",
       "2026-01-12 00:23:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens105_processed_ids_gene`\n",
       "2026-01-12 00:23:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens106_processed_ids_gene`\n",
       "2026-01-12 00:23:55 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens107_processed_ids_gene`\n",
       "2026-01-12 00:23:56 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens108_processed_ids_gene`\n",
       "2026-01-12 00:23:56 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens109_processed_ids_gene`\n",
       "2026-01-12 00:23:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens110_processed_ids_gene`\n",
       "2026-01-12 00:23:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens111_processed_ids_gene`\n",
       "2026-01-12 00:23:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens112_processed_ids_gene`\n",
       "2026-01-12 00:23:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens113_processed_ids_gene`\n",
       "2026-01-12 00:23:59 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens114_processed_ids_gene`\n",
       "2026-01-12 00:23:59 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_ids_gene`\n",
       "2026-01-12 00:24:00 INFO:graph_maker: Edges between versionless ID to version ID has been added for &#x27;gene&#x27;, assembly 111.\n",
       "2026-01-12 00:24:00 INFO:graph_maker: Synonymous external nodes are being merged into one.\n",
       "2026-01-12 00:24:00 INFO:graph_maker: Number of removed nodes in the process of merging synonymous nodes: 1290\n",
       "2026-01-12 00:24:07 INFO:graph_maker: The graph is being exported as &#x27;/Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_sus_scrofa_min48_max115_narrow.pickle&#x27;.\n",
       "2026-01-12 00:24:17 INFO:the_graph: Cached properties being calculated: available_genome_assemblies\n",
       "2026-01-12 00:24:17 INFO:the_graph: Cached properties being calculated: combined_edges\n",
       "2026-01-12 00:24:24 INFO:the_graph: Cached properties being calculated: combined_edges_genes\n",
       "2026-01-12 00:24:30 INFO:the_graph: Cached properties being calculated: combined_edges_assembly_specific_genes</pre>\n",
       "</details>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%%collapse Click to show build logs\n",
    "# Included for tutorial purposes only.\n",
    "\n",
    "# Build (or load) the pig graph snapshot\n",
    "if HAS_PIG_YAML:\n",
    "    api.build_graph(organism_name=organism, snapshot_release=SNAPSHOT_RELEASE, calculate_caches=False)\n",
    "else:\n",
    "    print('Skipping pig build: sus_scrofa_externals_modified.yml is missing (run Part 2 first).')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "41615ba1",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Organism: sus_scrofa\n",
      "Snapshot release: 115\n",
      "Main assembly: 111\n",
      "Assemblies in this graph: [9, 102, 111]\n",
      "Nodes: 1073214\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2026-01-12 00:24:32 INFO:the_graph: Cached properties being calculated: available_external_databases\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Edges: 1757774\n",
      "External DBs enabled (count): 24\n",
      "External DBs (first 20): ['Clone_based_ensembl_gene', 'Clone_based_vega_gene', 'EntrezGene', 'HGNC Symbol', 'Havana gene', 'Havana transcript', 'NCBI gene', 'NCBI gene (formerly Entrezgene)', 'RFAM', 'RefSeq_mRNA', 'RefSeq_mRNA_predicted', 'RefSeq_ncRNA', 'RefSeq_ncRNA_predicted', 'RefSeq_peptide', 'RefSeq_peptide_predicted', 'UniProtKB Gene Name', 'Uniprot/SPTREMBL', 'Uniprot/SWISSPROT', 'VGNC Symbol', 'synonym_id::EntrezGene']\n"
     ]
    }
   ],
   "source": [
    "if HAS_PIG_YAML:\n",
    "    g = api.track.graph\n",
    "    print('Organism:', g.graph.get('organism'))\n",
    "    print('Snapshot release:', g.graph.get('ensembl_release'))\n",
    "    print('Main assembly:', g.graph.get('genome_assembly'))\n",
    "    print('Assemblies in this graph:', sorted(api.list_genome_assemblies()))\n",
    "    print('Nodes:', g.number_of_nodes())\n",
    "    print('Edges:', g.number_of_edges())\n",
    "\n",
    "    aed = sorted(getattr(g, 'available_external_databases', []))\n",
    "    print('External DBs enabled (count):', len(aed))\n",
    "    print('External DBs (first 20):', aed[:20])\n",
    "else:\n",
    "    print('Pig graph not built (missing YAML).')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "ec692c7e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[PosixPath('/Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_sus_scrofa_min48_max115_narrow.pickle')]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sorted(LOCAL_REPOSITORY.glob('graph_sus_scrofa*.pickle'))[-5:]\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "52d4dbd4",
   "metadata": {},
   "source": [
    "## 3.4 — Graph management (all species)\n",
    "\n",
    "### Reloading vs rebuilding\n",
    "\n",
    "- `api.build_graph(...)` is safe to call repeatedly.\n",
    "  - If the snapshot already exists on disk, IDTrack will **load** it.\n",
    "  - If it does not exist yet, IDTrack will **build** it (slow, first-time only).\n",
    "\n",
    "### Cache hygiene\n",
    "\n",
    "Your local repository can accumulate:\n",
    "- downloaded tables\n",
    "- graph snapshot pickle files\n",
    "- intermediate files used during builds\n",
    "\n",
    "> **Tip:** Treat your local repository as *project infrastructure*. Keep it stable so you get the benefits of caching.\n",
    "\n",
    "### Switching organisms / assemblies\n",
    "\n",
    "A graph snapshot is specific to:\n",
    "- organism\n",
    "- snapshot boundary (max release)\n",
    "- external YAML contents\n",
    "- the chosen **primary assembly** (the default output coordinate system)\n",
    "\n",
    "Even though the snapshot can include multiple assemblies, changing the primary assembly changes the snapshot and requires a rebuild.\n",
    "\n",
    "> **Tip:** The cached graph filename does not include the assembly. If you want to keep two different primary assemblies side-by-side, use\n",
    "> separate local repositories (or copy the graph pickle file).\n",
    "\n",
    "### Performance tips\n",
    "\n",
    "- Use `calculate_caches=True` during builds when you plan to do many conversions afterward.\n",
    "- Keep your external YAML allowlist small to reduce ambiguity and search space.\n",
    "\n",
    "> **Warning:** Do not delete caches unless you understand the consequence (you may force a full rebuild).\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "9ee6e582",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Local repository: /Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache\n",
      "\n",
      "graph_*.pickle (3):\n",
      "   graph_homo_sapiens_min48_max115_narrow.pickle\n",
      "   graph_mus_musculus_min48_max115_narrow.pickle\n",
      "   graph_sus_scrofa_min48_max115_narrow.pickle\n",
      "\n",
      "*_externals_modified.yml (3):\n",
      "   homo_sapiens_externals_modified.yml\n",
      "   mus_musculus_externals_modified.yml\n",
      "   sus_scrofa_externals_modified.yml\n",
      "\n",
      "*_externals_template.yml (3):\n",
      "   homo_sapiens_externals_template.yml\n",
      "   mus_musculus_externals_template.yml\n",
      "   sus_scrofa_externals_template.yml\n"
     ]
    }
   ],
   "source": [
    "# Helper: list what IDTrack has cached in your local repository.\n",
    "# Safe: this does NOT delete anything.\n",
    "\n",
    "from pathlib import Path\n",
    "\n",
    "cache = LOCAL_REPOSITORY\n",
    "\n",
    "print('Local repository:', cache)\n",
    "\n",
    "patterns = [\n",
    "    'graph_*.pickle',\n",
    "    '*_externals_modified.yml',\n",
    "    '*_externals_template.yml',\n",
    "]\n",
    "\n",
    "for pat in patterns:\n",
    "    hits = sorted(cache.glob(pat))\n",
    "    print()\n",
    "    print(f'{pat} ({len(hits)}):')\n",
    "    for p in hits[:10]:\n",
    "        print('  ', p.name)\n",
    "    if len(hits) > 10:\n",
    "        print('  ...')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ae04c5be",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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