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#!/usr/bin/env python |
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# -*- coding: utf-8 -*- |
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""" |
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""" |
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from Bio import AlignIO |
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import argparse |
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from icecream import ic |
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import sys |
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ic.configureOutput(outputFunction=lambda *a: print(*a, file=sys.stderr)) |
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ic.configureOutput(prefix='> ') |
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def get_parser(): |
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parser = argparse.ArgumentParser( |
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description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) |
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parser.add_argument("-v", "--verbose", |
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action="store_true", help="be verbose") |
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parser.add_argument("sequence", help="", default="") # nargs='+') |
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parser.add_argument("stk", help="", default="") # nargs='+') |
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return parser |
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if __name__ == '__main__': |
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parser = get_parser() |
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args = parser.parse_args() |
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verbose = args.verbose |
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# Load the alignment |
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alignment = AlignIO.read(args.stk, "stockholm") |
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alignment_name = args.stk.split('/')[-1] |
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# Define the target sequence ID |
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target_id = args.sequence |
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# Find the target sequence |
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target_seq = None |
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for record in alignment: |
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if record.id == target_id: |
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target_seq = record.seq |
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break |
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if target_seq is None: |
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print(f"Target sequence '{target_id}' not found in the alignment.") |
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else: |
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seq_len = 0 |
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cols_no_coverage = 0 |
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# Collect columns where the target sequence has no gaps |
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filtered_columns = [] |
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for col_index in range(alignment.get_alignment_length()): |
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if target_seq[col_index] != "-": |
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column = [record.seq[col_index] for record in alignment] |
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filtered_columns.append(column) |
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seq_len += 1 |
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# Display filtered columns |
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if verbose: print(f"Columns where the target sequence '{target_id}' has no gaps:") |
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for col in filtered_columns: |
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if verbose: print(col, len(col)) |
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# Count the number of '-' |
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gap_count = col.count('-') |
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if verbose: print(f"Number of '-': {gap_count}") |
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ratio_per_col = gap_count/(len(col) - 1) |
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if verbose: print(f'ratio of gaps: {ratio_per_col}') # -1 target_sequence |
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if ratio_per_col > 0.5: |
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if verbose: print('WARNING: more than 50% gaps in column', cols_no_coverage) |
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cols_no_coverage +=1 |
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if verbose: print() |
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ratio = round((1 - (cols_no_coverage / seq_len)) * 100) |
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print(f"Query {target_id} length {seq_len} in the alignment {alignment_name} number of columns with low coverage (<50%) for the query sequence {cols_no_coverage}; coverge for the query: {ratio}%") |
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mmagnus /
rna-tools
