file_utils.py 文件源码

def IndexedVariantFileReader(phenocode):
    filepath = common_filepaths['pheno_gz'](phenocode)

    with read_gzip(filepath) as f:
        reader = csv.reader(f, dialect='pheweb-internal-dialect')
        colnames = next(reader)
    assert colnames[0].startswith('#')
    colnames[0] = colnames[0][1:]
    for field in colnames:
        assert field in conf.parse.per_variant_fields or field in conf.parse.per_assoc_fields, (field)
    colidxs = {field: colnum for colnum, field in enumerate(colnames)}

    with pysam.TabixFile(filepath, parser=None) as tabix_file:
        yield _ivfr(tabix_file, colidxs)