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Add a Jupyter Notebook for Babel #622

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204 changes: 204 additions & 0 deletions docs/Babel.ipynb
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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "14afaf6a-3ee7-42db-8881-4e158fe933fe",
"metadata": {},
"outputs": [],
"source": [
"# Babel"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "9a18b461-6c0e-43fa-bf28-68dc8720adf5",
"metadata": {},
"outputs": [],
"source": [
"import os\n",
"import subprocess\n",
"\n",
"os.chdir(\"..\")"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "79ee7d5c-f1da-4a19-985f-2ea00e1c0361",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"/Users/gaurav/Developer/translator/babel\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Assuming unrestricted shared filesystem usage.\n",
"INFO snakemake.logging [2025-12-10T08:23:37-0500]: Assuming unrestricted shared filesystem usage.\n",
"INFO snakemake.logging [2025-12-10T08:23:37-0500]: None\n",
"host: Ashman.local\n",
"INFO snakemake.logging [2025-12-10T08:23:37-0500]: host: Ashman.local\n",
"Building DAG of jobs...\n",
"INFO snakemake.logging [2025-12-10T08:23:37-0500]: Building DAG of jobs...\n",
"Using shell: /opt/homebrew/bin/bash\n",
"INFO snakemake.logging [2025-12-10T08:23:37-0500]: Using shell: /opt/homebrew/bin/bash\n",
"Provided cores: 5\n",
"INFO snakemake.logging [2025-12-10T08:23:37-0500]: Provided cores: 5\n",
"Rules claiming more threads will be scaled down.\n",
"INFO snakemake.logging [2025-12-10T08:23:37-0500]: Rules claiming more threads will be scaled down.\n",
"Job stats:\n",
"job count\n",
"----------------------------------------- -------\n",
"check_macromolecular_complex 1\n",
"check_macromolecular_complex_completeness 1\n",
"macromolecular_complex 1\n",
"total 3\n",
"\n",
"INFO snakemake.logging [2025-12-10T08:23:37-0500]: Job stats:\n",
"job count\n",
"----------------------------------------- -------\n",
"check_macromolecular_complex 1\n",
"check_macromolecular_complex_completeness 1\n",
"macromolecular_complex 1\n",
"total 3\n",
"\n",
"Select jobs to execute...\n",
"INFO snakemake.logging [2025-12-10T08:23:37-0500]: Select jobs to execute...\n",
"Execute 2 jobs...\n",
"INFO snakemake.logging [2025-12-10T08:23:37-0500]: Execute 2 jobs...\n",
"\n",
"[Wed Dec 10 03:23:37 2025]\n",
"localrule check_macromolecular_complex_completeness:\n",
" input: babel_outputs/compendia/MacromolecularComplex.txt\n",
" output: babel_outputs/reports/macromolecular_complex_completeness.txt\n",
" jobid: 9\n",
" reason: Updated input files: babel_outputs/compendia/MacromolecularComplex.txt\n",
" resources: tmpdir=/var/folders/xk/0z8klmh13x35_vp_vkzd_yf00000gn/T\n",
"INFO snakemake.logging [2025-12-10T08:23:37-0500]: Rule: check_macromolecular_complex_completeness, Jobid: 9\n",
"INFO snakemake.logging [2025-12-10T08:23:37-0500]: Shell command: None\n",
"[Wed Dec 10 03:23:37 2025]\n",
"localrule check_macromolecular_complex:\n",
" input: babel_outputs/compendia/MacromolecularComplex.txt\n",
" output: babel_outputs/reports/MacromolecularComplex.txt\n",
" jobid: 10\n",
" reason: Updated input files: babel_outputs/compendia/MacromolecularComplex.txt\n",
" resources: tmpdir=/var/folders/xk/0z8klmh13x35_vp_vkzd_yf00000gn/T\n",
"INFO snakemake.logging [2025-12-10T08:23:37-0500]: Rule: check_macromolecular_complex, Jobid: 10\n",
"INFO snakemake.logging [2025-12-10T08:23:37-0500]: Shell command: None\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"babel_outputs/compendia/MacromolecularComplex.txt\n",
"Missing identifiers: 0\n",
"\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"[Wed Dec 10 03:23:39 2025]\n",
"Finished jobid: 9 (Rule: check_macromolecular_complex_completeness)\n",
"INFO snakemake.logging [2025-12-10T08:23:39-0500]: Finished jobid: 9 (Rule: check_macromolecular_complex_completeness)\n",
"1 of 3 steps (33%) done\n",
"INFO snakemake.logging [2025-12-10T08:23:39-0500]: None\n",
"[Wed Dec 10 03:23:39 2025]\n",
"Finished jobid: 10 (Rule: check_macromolecular_complex)\n",
"INFO snakemake.logging [2025-12-10T08:23:39-0500]: Finished jobid: 10 (Rule: check_macromolecular_complex)\n",
"2 of 3 steps (67%) done\n",
"INFO snakemake.logging [2025-12-10T08:23:39-0500]: None\n",
"Select jobs to execute...\n",
"INFO snakemake.logging [2025-12-10T08:23:39-0500]: Select jobs to execute...\n",
"Execute 1 jobs...\n",
"INFO snakemake.logging [2025-12-10T08:23:39-0500]: Execute 1 jobs...\n",
"\n",
"[Wed Dec 10 03:23:39 2025]\n",
"localrule macromolecular_complex:\n",
" input: babel_outputs/synonyms/MacromolecularComplex.txt, babel_outputs/metadata/MacromolecularComplex.txt.yaml, babel_outputs/reports/macromolecular_complex_completeness.txt, babel_outputs/reports/MacromolecularComplex.txt\n",
" output: babel_outputs/synonyms/MacromolecularComplex.txt.gz, babel_outputs/reports/macromolecular_complex_done\n",
" jobid: 0\n",
" reason: Input files updated by another job: babel_outputs/reports/macromolecular_complex_completeness.txt, babel_outputs/reports/MacromolecularComplex.txt\n",
" resources: tmpdir=/var/folders/xk/0z8klmh13x35_vp_vkzd_yf00000gn/T\n",
"INFO snakemake.logging [2025-12-10T08:23:39-0500]: Rule: macromolecular_complex, Jobid: 0\n",
"INFO snakemake.logging [2025-12-10T08:23:39-0500]: Shell command: None\n",
"gzip_files: Compressing: ['babel_outputs/synonyms/MacromolecularComplex.txt']\n",
"INFO src.snakefiles.util [2025-12-10T08:23:39-0500]: Compressing: ['babel_outputs/synonyms/MacromolecularComplex.txt']\n",
"gzip_files: Compressed babel_outputs/synonyms/MacromolecularComplex.txt to babel_outputs/synonyms/MacromolecularComplex.txt.gz using the gzip module.\n",
"INFO src.snakefiles.util [2025-12-10T08:23:39-0500]: Compressed babel_outputs/synonyms/MacromolecularComplex.txt to babel_outputs/synonyms/MacromolecularComplex.txt.gz using the gzip module.\n",
"gzip_files: Done compressing: ['babel_outputs/synonyms/MacromolecularComplex.txt']\n",
"INFO src.snakefiles.util [2025-12-10T08:23:39-0500]: Done compressing: ['babel_outputs/synonyms/MacromolecularComplex.txt']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"done <_io.TextIOWrapper name='babel_outputs/reports/macromolecular_complex_done' mode='w' encoding='UTF-8'>\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"[Wed Dec 10 03:23:40 2025]\n",
"Finished jobid: 0 (Rule: macromolecular_complex)\n",
"INFO snakemake.logging [2025-12-10T08:23:40-0500]: Finished jobid: 0 (Rule: macromolecular_complex)\n",
"3 of 3 steps (100%) done\n",
"INFO snakemake.logging [2025-12-10T08:23:40-0500]: None\n",
"Removing temporary output babel_outputs/synonyms/MacromolecularComplex.txt.\n",
"INFO snakemake.logging [2025-12-10T08:23:40-0500]: Removing temporary output babel_outputs/synonyms/MacromolecularComplex.txt.\n",
"Complete log(s): /Users/gaurav/Developer/translator/babel/.snakemake/log/2025-12-10T032336.775363.snakemake.log\n",
"INFO snakemake.logging [2025-12-10T08:23:40-0500]: Complete log(s): /Users/gaurav/Developer/translator/babel/.snakemake/log/2025-12-10T032336.775363.snakemake.log\n"
]
},
{
"data": {
"text/plain": [
"CompletedProcess(args=['uv', 'run', 'snakemake', '-c', '5', 'macromolecular_complex'], returncode=0)"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"CORES=5\n",
"\n",
"print(os.getcwd())\n",
"subprocess.run([\"uv\", \"run\", \"snakemake\", \"-c\", str(CORES), \"macromolecular_complex\"])"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.14.0"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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