Added a separate AlignmentRunner for handling seq_emb mode.
- In `seq_emb` mode, the AlignmentRunner works only on generating templates.
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@ -73,17 +73,26 @@ def precompute_alignments(tags, seqs, alignment_dir, args):
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os.makedirs(local_alignment_dir)
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alignment_runner = data_pipeline.AlignmentRunner(
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jackhmmer_binary_path=args.jackhmmer_binary_path,
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hhblits_binary_path=args.hhblits_binary_path,
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hhsearch_binary_path=args.hhsearch_binary_path,
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uniref90_database_path=args.uniref90_database_path,
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mgnify_database_path=args.mgnify_database_path,
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bfd_database_path=args.bfd_database_path,
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uniclust30_database_path=args.uniclust30_database_path,
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pdb70_database_path=args.pdb70_database_path,
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no_cpus=args.cpus,
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)
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if args.use_single_seq_mode:
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alignment_runner = data_pipeline.AlignmentRunner(
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jackhmmer_binary_path=args.jackhmmer_binary_path,
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hhsearch_binary_path=args.hhsearch_binary_path,
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uniref90_database_path=args.uniref90_database_path,
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pdb70_database_path=args.pdb70_database_path,
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no_cpus=args.cpus,
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)
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else:
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alignment_runner = data_pipeline.AlignmentRunner(
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jackhmmer_binary_path=args.jackhmmer_binary_path,
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hhblits_binary_path=args.hhblits_binary_path,
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hhsearch_binary_path=args.hhsearch_binary_path,
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uniref90_database_path=args.uniref90_database_path,
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mgnify_database_path=args.mgnify_database_path,
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bfd_database_path=args.bfd_database_path,
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uniclust30_database_path=args.uniclust30_database_path,
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pdb70_database_path=args.pdb70_database_path,
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no_cpus=args.cpus,
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)
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alignment_runner.run(
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tmp_fasta_path, local_alignment_dir
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)
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