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''' |
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Converts .sto alignment format to .a2m format. |
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''' |
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import argparse |
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from evcouplings.align.alignment import Alignment |
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from evcouplings.align.protocol import modify_alignment, cut_sequence |
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import numpy as np |
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from utils import read_fasta |
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def main(): |
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parser = argparse.ArgumentParser() |
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parser.add_argument('target_seq_file', type=str, |
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help='input filepath for the target sequence in fasta') |
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parser.add_argument('sto_alignment_file', type=str, help='input filepath for .sto') |
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parser.add_argument('output_prefix', type=str, help='output filepath prefix') |
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args = parser.parse_args() |
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with open(args.sto_alignment_file) as a: |
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ali_raw = Alignment.from_file(a, "stockholm") |
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focus_cols = np.array([c != "-" for c in ali_raw[0]]) |
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focus_ali = ali_raw.select(columns=focus_cols) |
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target_seq, target_id = read_fasta(args.target_seq_file, return_ids=True) |
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assert len(target_seq) == 1, 'more than 1 target seq' |
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target_seq = target_seq[0] |
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target_id = target_id[0] |
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assert len(target_seq) == len(focus_ali[0]), ( |
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f'{len(focus_cols)} focus cols, expected {len(target_seq)}') |
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target_seq_index = 0 |
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region_start = 0 |
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kwargs = { |
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'prefix': args.output_prefix, |
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'seqid_filter': None, |
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'hhfilter': None, |
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'minimum_sequence_coverage': 50, |
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'minimum_column_coverage': 70, |
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'compute_num_effective_seqs': False, |
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'theta': 0.8, |
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} |
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mod_outcfg, ali = modify_alignment( |
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focus_ali, target_seq_index, target_id, region_start, **kwargs) |
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if __name__ == "__main__": |
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main() |
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