mirror of
https://github.com/KosinskiLab/AlphaPulldown.git
synced 2026-06-04 14:14:24 +08:00
4d802be7d6
* symmetrical refactoring to support both af2 and af3 data pipelines * Clean tests * Keep GPU tests in place * Reverted accidentally deleted templates * Add AlphaFold3 feature creation pipeline and per-chain input generation - Implement `create_pipeline_af3` to construct the AlphaFold3 data pipeline with correct database and binary paths. - Add `create_af3_individual_features` to generate AlphaFold3 input features for each chain in a FASTA, handling protein, RNA, and DNA sequences. - Integrate new AF3 logic into the main entry point, dispatching to AF2 or AF3 as appropriate. - Ensure output directory creation and error handling for missing dependencies or invalid sequences. * Convert template dates to datetime for af3 * First check for nucleotides, then for amino-acids * Skip existing features json if --skip_existing=true * Check if DNA before RNA * Bump 2.1.0 * Git ignore build/ dir
103 lines
3.6 KiB
Python
103 lines
3.6 KiB
Python
import subprocess
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from pathlib import Path
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from absl.testing import absltest
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import alphapulldown.scripts.create_individual_features as run_features_generation
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import tempfile
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import time
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import os
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class TestCreateIndividualFeaturesWithTemplates(absltest.TestCase):
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def setUp(self):
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super().setUp()
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self.temp_dir = tempfile.TemporaryDirectory()
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self.TEST_DATA_DIR = Path(self.temp_dir.name)
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self.TEST_DATA_DIR = Path('debug')
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self.logs = self.TEST_DATA_DIR / "logs"
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self.logs.mkdir(parents=True, exist_ok=True)
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self.fasta_file = Path(__file__).parent / "test_data" / "true_multimer" / "fastas" / "3L4Q.fa"
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def tearDown(self):
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print(self.TEST_DATA_DIR)
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print(os.listdir(self.TEST_DATA_DIR))
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self.temp_dir.cleanup()
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def generate_slurm_script(self):
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slurm_script_content = \
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f"""#!/bin/bash
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#SBATCH --job-name=array
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#SBATCH --time=10:00:00
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#SBATCH -e {self.logs}/create_individual_features_%A_%a_err.txt
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#SBATCH -o {self.logs}/create_individual_features_%A_%a_out.txt
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#SBATCH --qos=low
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#SBATCH -N 1
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#SBATCH --ntasks=8
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#SBATCH --mem=32000
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#module load Anaconda3
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eval "$(conda shell.bash hook)"
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conda activate AlphaPulldown
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SEQ_INDEX=${{SLURM_ARRAY_TASK_ID:-1}}
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USE_MMSEQS2=False
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if [ "$SEQ_INDEX" -eq 1 ] || [ "$SEQ_INDEX" -eq 3 ]; then
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USE_MMSEQS2=True
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fi
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python {run_features_generation.__file__} \\
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--use_precomputed_msas False \\
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--save_msa_files True \\
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--skip_existing False \\
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--data_dir /scratch/AlphaFold_DBs/2.3.2 \\
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--max_template_date 3021-01-01 \\
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--fasta_paths {self.fasta_file} \\
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--output_dir {self.TEST_DATA_DIR}/features_mmseqs_${{USE_MMSEQS2}} \\
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--seq_index ${{SEQ_INDEX}} \\
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--use_mmseqs2 ${{USE_MMSEQS2}}
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"""
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script_file = Path(self.TEST_DATA_DIR) / "run_feature_generation.slurm"
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with open(script_file, 'w') as file:
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file.write(slurm_script_content)
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return script_file
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def submit_slurm_job(self, script_file):
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command = ['sbatch', '--array=1-4', str(script_file)]
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result = subprocess.run(command, capture_output=True, text=True, check=True)
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job_id = result.stdout.strip().split()[-1] # Assumes sbatch output is "Submitted batch job <job_id>"
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return job_id
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def wait_for_slurm_jobs_to_finish(self, job_id, polling_interval=60):
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"""Polls squeue and waits for the job to no longer be listed."""
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while True:
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result = subprocess.run(['squeue', '--job', job_id], capture_output=True, text=True)
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if job_id not in result.stdout:
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break # Job has finished
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time.sleep(polling_interval)
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def compare_output_files(self):
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for prefix in ["True", "False"]:
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if prefix == 'True':
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for protein in ["3L4Q_A_mmseqs.pkl", "3L4Q_C_mmseqs.pkl"]:
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assert (self.TEST_DATA_DIR / f"features_mmseqs_{prefix}" / protein).exists()
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if prefix == 'False':
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for protein in ["3L4Q_A.pkl", "3L4Q_C.pkl"]:
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assert (self.TEST_DATA_DIR / f"features_mmseqs_{prefix}" / protein).exists()
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@absltest.skip("Skipping this test for now")
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def test_run_features_generation_all_parallel(self):
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slurm_script_file = self.generate_slurm_script()
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print(f"SLURM script generated at: {slurm_script_file}")
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job_id = self.submit_slurm_job(slurm_script_file)
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print(f"Submitted SLURM job {job_id}")
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self.wait_for_slurm_jobs_to_finish(job_id)
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print("All SLURM jobs have completed.")
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self.compare_output_files()
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if __name__ == '__main__':
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absltest.main()
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