2024-03-05 06:38:17 +00:00
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import os
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from hydra import initialize, compose
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from pathlib import Path
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import subprocess
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#from rf2aa.run_inference import ModelRunner
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def make_msa(
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fasta_file,
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2024-03-06 00:45:27 +00:00
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chain,
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2024-03-05 06:38:17 +00:00
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model_runner
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):
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out_dir_base = Path(model_runner.config.output_path)
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hash = model_runner.config.job_name
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2024-03-06 00:45:27 +00:00
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out_dir = out_dir_base / hash / chain
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2024-03-05 06:38:17 +00:00
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out_dir.mkdir(parents=True, exist_ok=True)
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command = model_runner.config.database_params.command
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search_base = model_runner.config.database_params.sequencedb
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num_cpus = model_runner.config.database_params.num_cpus
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ram_gb = model_runner.config.database_params.mem
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template_database = model_runner.config.database_params.hhdb
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out_a3m = out_dir / "t000_.msa0.a3m"
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out_atab = out_dir / "t000_.atab"
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out_hhr = out_dir / "t000_.hhr"
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if out_a3m.exists() and out_atab.exists() and out_hhr.exists():
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return out_a3m, out_hhr, out_atab
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search_command = f"./{command} {fasta_file} {out_dir} {num_cpus} {ram_gb} {search_base} {template_database}"
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print(search_command)
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_ = subprocess.run(search_command, shell=True)
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return out_a3m, out_hhr, out_atab
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