Speed up data loading process #376
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added 11 commits
November 30, 2023 11:51
christinaflo
reviewed
Dec 8, 2023
| parser.add_argument('--alignment_dir', type=str, help='path to alignment dir') | ||
| args = parser.parse_args() | ||
| alignment_dir = args.alignment_dir | ||
| stockholm_files = [i for i in os.listdir(alignment_dir) if (i.endswith('.sto') and ("hmm_output" not in i))] |
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here can you add an exclusion "uniprot_hits" as well? I changed this recently, it is only used for msa pairing.
christinaflo
reviewed
Dec 8, 2023
| continue | ||
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| msa_data[f] = msa | ||
| # Now will split the following steps into multiple processes |
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If we already generated the pkl file, then we should check that it exists before re-parsing the msas. Or does it get removed somewhere?
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Oh also, is there reason we couldn't just call a function to do this instead of running the script with subprocess?
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Now MSA files are parsed in parallel instead of in serial way