INNER CODE UNIT · Python

parse_straglr_tsv

BirolLab/straglr · straglr_compare.py:43

def parse_straglr_tsv(tsv, use_size=True, skip_chroms=None, old_version=False):
    alleles = {}
    with open(tsv, 'r') as ff:
        for line in ff:
            if line[0] == '#':
                continue

            cols = line.rstrip().split('\t')
            if not old_version and cols[-1] != 'full':
                continue
            
            if skip_chroms is not None and cols[0] in skip_chroms:
                continue
            locus = cols[:4]
            # coordinate error in straglr output
            if int(locus[1]) > int(locus[2]):
                continue
            ref_size = int(cols[2]) - int(cols[1]) + 1

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