Tabix (pysam)¶
- petlx.tabix.fromtabix(filename, reference=None, start=None, end=None, region=None, header=None)[source]¶
Extract rows from a tabix indexed file. E.g.:
>>> from petlx.tabix import fromtabix >>> from petl import look >>> t = fromtabix('test.bed.gz', region='Pf3D7_02_v3:100000-200000') >>> look(t) +---------------+----------+----------+-----------------------------+ | '#chrom' | 'start' | 'end' | 'region' | +===============+==========+==========+=============================+ | 'Pf3D7_02_v3' | '23100' | '105800' | 'SubtelomericHypervariable' | +---------------+----------+----------+-----------------------------+ | 'Pf3D7_02_v3' | '105800' | '447300' | 'Core' | +---------------+----------+----------+-----------------------------+
New in version 0.4.