Commit ba025f57 authored by Weipeng Mo's avatar Weipeng Mo
Browse files

fix bugs

parent a6cb6db4
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+4 −2
Original line number Diff line number Diff line
@@ -64,11 +64,11 @@ def get_record_range(invs,

def get_gtf_attribute(gtf_record, attribute):
    try:
        attr = re.search(f'{attribute} "(.+?)";', gtf_record[8]).group(1)
        attr = re.search(f'{attribute} "(.+?)"', gtf_record[8]).group(1)
    except AttributeError:
        raise ValueError(
            f'Could not parse attribute {attribute} '
            f'from GTF with feature type {record[2]}'
            f'from GTF with feature type {gtf_record[2]}'
        )
    return attr

@@ -85,6 +85,8 @@ def gtf_iterator(gtf_fn,
        gene_to_locus_mapping = {}
    with open(gtf_fn) as gtf:
        for i, record in enumerate(gtf):
            if record.startswith('#'):
                continue
            record = record.split('\t')
            chrom, _, feat_type, start, end, _, strand = record[:7]
            start = int(start) - 1