Variant call format (PyVCF)¶
- petlx.vcf.fromvcf(filename, chrom=None, start=None, end=None, samples=True)[source]¶
Returns a table providing access to data from a variant call file (VCF). E.g.:
>>> from petl import look >>> from petlx.vcf import fromvcf >>> t = fromvcf('example.vcf') >>> look(t) +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+---------------------------------------------------------------------+------------------------------------------------------------------+----------------------------------------------------------------------+ | 'CHROM' | 'POS' | 'ID' | 'REF' | 'ALT' | 'QUAL' | 'FILTER' | 'INFO' | 'NA00001' | 'NA00002' | 'NA00003' | +=========+=========+=============+=======+===========+========+==========+=========================================================================================+=====================================================================+==================================================================+======================================================================+ | '19' | 111 | None | 'A' | [C] | 9.6 | [] | {} | Call(sample=NA00001, CallData(GT=0|0, HQ=[10, 10])) | Call(sample=NA00002, CallData(GT=0|0, HQ=[10, 10])) | Call(sample=NA00003, CallData(GT=0/1, HQ=[3, 3])) | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+---------------------------------------------------------------------+------------------------------------------------------------------+----------------------------------------------------------------------+ | '19' | 112 | None | 'A' | [G] | 10 | [] | {} | Call(sample=NA00001, CallData(GT=0|0, HQ=[10, 10])) | Call(sample=NA00002, CallData(GT=0|0, HQ=[10, 10])) | Call(sample=NA00003, CallData(GT=0/1, HQ=[3, 3])) | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+---------------------------------------------------------------------+------------------------------------------------------------------+----------------------------------------------------------------------+ | '20' | 14370 | 'rs6054257' | 'G' | [A] | 29 | [] | OrderedDict([('NS', 3), ('DP', 14), ('AF', [0.5]), ('DB', True), ('H2', True)]) | Call(sample=NA00001, CallData(GT=0|0, GQ=48, DP=1, HQ=[51, 51])) | Call(sample=NA00002, CallData(GT=1|0, GQ=48, DP=8, HQ=[51, 51])) | Call(sample=NA00003, CallData(GT=1/1, GQ=43, DP=5, HQ=[None, None])) | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+---------------------------------------------------------------------+------------------------------------------------------------------+----------------------------------------------------------------------+ | '20' | 17330 | None | 'T' | [A] | 3 | ['q10'] | OrderedDict([('NS', 3), ('DP', 11), ('AF', [0.017])]) | Call(sample=NA00001, CallData(GT=0|0, GQ=49, DP=3, HQ=[58, 50])) | Call(sample=NA00002, CallData(GT=0|1, GQ=3, DP=5, HQ=[65, 3])) | Call(sample=NA00003, CallData(GT=0/0, GQ=41, DP=3, HQ=[None, None])) | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+---------------------------------------------------------------------+------------------------------------------------------------------+----------------------------------------------------------------------+ | '20' | 1110696 | 'rs6040355' | 'A' | [G, T] | 67 | [] | OrderedDict([('NS', 2), ('DP', 10), ('AF', [0.333, 0.667]), ('AA', 'T'), ('DB', True)]) | Call(sample=NA00001, CallData(GT=1|2, GQ=21, DP=6, HQ=[23, 27])) | Call(sample=NA00002, CallData(GT=2|1, GQ=2, DP=0, HQ=[18, 2])) | Call(sample=NA00003, CallData(GT=2/2, GQ=35, DP=4, HQ=[None, None])) | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+---------------------------------------------------------------------+------------------------------------------------------------------+----------------------------------------------------------------------+ | '20' | 1230237 | None | 'T' | [None] | 47 | [] | OrderedDict([('NS', 3), ('DP', 13), ('AA', 'T')]) | Call(sample=NA00001, CallData(GT=0|0, GQ=54, DP=None, HQ=[56, 60])) | Call(sample=NA00002, CallData(GT=0|0, GQ=48, DP=4, HQ=[51, 51])) | Call(sample=NA00003, CallData(GT=0/0, GQ=61, DP=2, HQ=[None, None])) | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+---------------------------------------------------------------------+------------------------------------------------------------------+----------------------------------------------------------------------+ | '20' | 1234567 | 'microsat1' | 'G' | [GA, GAC] | 50 | [] | OrderedDict([('NS', 3), ('DP', 9), ('AA', 'G'), ('AN', 6), ('AC', [3, 1])]) | Call(sample=NA00001, CallData(GT=0/1, GQ=None, DP=4)) | Call(sample=NA00002, CallData(GT=0/2, GQ=17, DP=2)) | Call(sample=NA00003, CallData(GT=None, GQ=40, DP=3)) | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+---------------------------------------------------------------------+------------------------------------------------------------------+----------------------------------------------------------------------+ | '20' | 1235237 | None | 'T' | [None] | None | [] | {} | Call(sample=NA00001, CallData(GT=0/0)) | Call(sample=NA00002, CallData(GT=0|0)) | Call(sample=NA00003, CallData(GT=None)) | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+---------------------------------------------------------------------+------------------------------------------------------------------+----------------------------------------------------------------------+ | 'X' | 10 | 'rsTest' | 'AC' | [A, ATG] | 10 | [] | {} | Call(sample=NA00001, CallData(GT=0)) | Call(sample=NA00002, CallData(GT=0/1)) | Call(sample=NA00003, CallData(GT=0|2)) | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+---------------------------------------------------------------------+------------------------------------------------------------------+----------------------------------------------------------------------+
New in version 0.5.
- petlx.vcf.unpackinfo(tbl, *keys, **kwargs)[source]¶
Unpack the INFO field into separate fields. E.g.:
>>> from petlx.vcf import fromvcf, unpackinfo >>> from petl import look >>> t1 = fromvcf('../fixture/sample.vcf', samples=False) >>> look(t1) +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+ | 'CHROM' | 'POS' | 'ID' | 'REF' | 'ALT' | 'QUAL' | 'FILTER' | 'INFO' | +=========+=========+=============+=======+===========+========+==========+=========================================================================================+ | '19' | 111 | None | 'A' | [C] | 9.6 | [] | {} | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+ | '19' | 112 | None | 'A' | [G] | 10 | [] | {} | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+ | '20' | 14370 | 'rs6054257' | 'G' | [A] | 29 | [] | OrderedDict([('NS', 3), ('DP', 14), ('AF', [0.5]), ('DB', True), ('H2', True)]) | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+ | '20' | 17330 | None | 'T' | [A] | 3 | ['q10'] | OrderedDict([('NS', 3), ('DP', 11), ('AF', [0.017])]) | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+ | '20' | 1110696 | 'rs6040355' | 'A' | [G, T] | 67 | [] | OrderedDict([('NS', 2), ('DP', 10), ('AF', [0.333, 0.667]), ('AA', 'T'), ('DB', True)]) | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+ | '20' | 1230237 | None | 'T' | [None] | 47 | [] | OrderedDict([('NS', 3), ('DP', 13), ('AA', 'T')]) | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+ | '20' | 1234567 | 'microsat1' | 'G' | [GA, GAC] | 50 | [] | OrderedDict([('NS', 3), ('DP', 9), ('AA', 'G'), ('AN', 6), ('AC', [3, 1])]) | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+ | '20' | 1235237 | None | 'T' | [None] | None | [] | {} | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+ | 'X' | 10 | 'rsTest' | 'AC' | [A, ATG] | 10 | [] | {} | +---------+---------+-------------+-------+-----------+--------+----------+-----------------------------------------------------------------------------------------+ >>> t2 = unpackinfo(t1) >>> look(t2) +---------+---------+-------------+-------+-----------+--------+----------+------+------+--------+------+----------------+------+------+------+ | 'CHROM' | 'POS' | 'ID' | 'REF' | 'ALT' | 'QUAL' | 'FILTER' | 'NS' | 'AN' | 'AC' | 'DP' | 'AF' | 'AA' | 'DB' | 'H2' | +=========+=========+=============+=======+===========+========+==========+======+======+========+======+================+======+======+======+ | '19' | 111 | None | 'A' | [C] | 9.6 | [] | None | None | None | None | None | None | None | None | +---------+---------+-------------+-------+-----------+--------+----------+------+------+--------+------+----------------+------+------+------+ | '19' | 112 | None | 'A' | [G] | 10 | [] | None | None | None | None | None | None | None | None | +---------+---------+-------------+-------+-----------+--------+----------+------+------+--------+------+----------------+------+------+------+ | '20' | 14370 | 'rs6054257' | 'G' | [A] | 29 | [] | 3 | None | None | 14 | [0.5] | None | True | True | +---------+---------+-------------+-------+-----------+--------+----------+------+------+--------+------+----------------+------+------+------+ | '20' | 17330 | None | 'T' | [A] | 3 | ['q10'] | 3 | None | None | 11 | [0.017] | None | None | None | +---------+---------+-------------+-------+-----------+--------+----------+------+------+--------+------+----------------+------+------+------+ | '20' | 1110696 | 'rs6040355' | 'A' | [G, T] | 67 | [] | 2 | None | None | 10 | [0.333, 0.667] | 'T' | True | None | +---------+---------+-------------+-------+-----------+--------+----------+------+------+--------+------+----------------+------+------+------+ | '20' | 1230237 | None | 'T' | [None] | 47 | [] | 3 | None | None | 13 | None | 'T' | None | None | +---------+---------+-------------+-------+-----------+--------+----------+------+------+--------+------+----------------+------+------+------+ | '20' | 1234567 | 'microsat1' | 'G' | [GA, GAC] | 50 | [] | 3 | 6 | [3, 1] | 9 | None | 'G' | None | None | +---------+---------+-------------+-------+-----------+--------+----------+------+------+--------+------+----------------+------+------+------+ | '20' | 1235237 | None | 'T' | [None] | None | [] | None | None | None | None | None | None | None | None | +---------+---------+-------------+-------+-----------+--------+----------+------+------+--------+------+----------------+------+------+------+ | 'X' | 10 | 'rsTest' | 'AC' | [A, ATG] | 10 | [] | None | None | None | None | None | None | None | None | +---------+---------+-------------+-------+-----------+--------+----------+------+------+--------+------+----------------+------+------+------+
New in version 0.5.
- petlx.vcf.meltsamples(tbl, *samples)[source]¶
Melt the samples columns. E.g.:
>>> from petlx.vcf import fromvcf, unpackinfo, meltsamples >>> from petl import look, cutout >>> t1 = fromvcf('../fixture/sample.vcf') >>> t2 = meltsamples(t1) >>> t3 = cutout(t2, 'INFO') >>> look(t3) +---------+-------+-------------+-------+-------+--------+----------+-----------+----------------------------------------------------------------------+ | 'CHROM' | 'POS' | 'ID' | 'REF' | 'ALT' | 'QUAL' | 'FILTER' | 'SAMPLE' | 'CALL' | +=========+=======+=============+=======+=======+========+==========+===========+======================================================================+ | '19' | 111 | None | 'A' | [C] | 9.6 | [] | 'NA00001' | Call(sample=NA00001, CallData(GT=0|0, HQ=[10, 10])) | +---------+-------+-------------+-------+-------+--------+----------+-----------+----------------------------------------------------------------------+ | '19' | 111 | None | 'A' | [C] | 9.6 | [] | 'NA00002' | Call(sample=NA00002, CallData(GT=0|0, HQ=[10, 10])) | +---------+-------+-------------+-------+-------+--------+----------+-----------+----------------------------------------------------------------------+ | '19' | 111 | None | 'A' | [C] | 9.6 | [] | 'NA00003' | Call(sample=NA00003, CallData(GT=0/1, HQ=[3, 3])) | +---------+-------+-------------+-------+-------+--------+----------+-----------+----------------------------------------------------------------------+ | '19' | 112 | None | 'A' | [G] | 10 | [] | 'NA00001' | Call(sample=NA00001, CallData(GT=0|0, HQ=[10, 10])) | +---------+-------+-------------+-------+-------+--------+----------+-----------+----------------------------------------------------------------------+ | '19' | 112 | None | 'A' | [G] | 10 | [] | 'NA00002' | Call(sample=NA00002, CallData(GT=0|0, HQ=[10, 10])) | +---------+-------+-------------+-------+-------+--------+----------+-----------+----------------------------------------------------------------------+ | '19' | 112 | None | 'A' | [G] | 10 | [] | 'NA00003' | Call(sample=NA00003, CallData(GT=0/1, HQ=[3, 3])) | +---------+-------+-------------+-------+-------+--------+----------+-----------+----------------------------------------------------------------------+ | '20' | 14370 | 'rs6054257' | 'G' | [A] | 29 | [] | 'NA00001' | Call(sample=NA00001, CallData(GT=0|0, GQ=48, DP=1, HQ=[51, 51])) | +---------+-------+-------------+-------+-------+--------+----------+-----------+----------------------------------------------------------------------+ | '20' | 14370 | 'rs6054257' | 'G' | [A] | 29 | [] | 'NA00002' | Call(sample=NA00002, CallData(GT=1|0, GQ=48, DP=8, HQ=[51, 51])) | +---------+-------+-------------+-------+-------+--------+----------+-----------+----------------------------------------------------------------------+ | '20' | 14370 | 'rs6054257' | 'G' | [A] | 29 | [] | 'NA00003' | Call(sample=NA00003, CallData(GT=1/1, GQ=43, DP=5, HQ=[None, None])) | +---------+-------+-------------+-------+-------+--------+----------+-----------+----------------------------------------------------------------------+ | '20' | 17330 | None | 'T' | [A] | 3 | ['q10'] | 'NA00001' | Call(sample=NA00001, CallData(GT=0|0, GQ=49, DP=3, HQ=[58, 50])) | +---------+-------+-------------+-------+-------+--------+----------+-----------+----------------------------------------------------------------------+
New in version 0.5.
- petlx.vcf.unpackcall(tbl, *keys, **kwargs)[source]¶
Unpack the call column. E.g.:
>>> from petlx.vcf import fromvcf, unpackinfo, meltsamples, unpackcall >>> from petl import look, cutout >>> t1 = fromvcf('../fixture/sample.vcf') >>> t2 = meltsamples(t1) >>> t3 = unpackcall(t2) >>> t4 = cutout(t3, 'INFO') >>> look(t4) +---------+-------+-------------+-------+-------+--------+----------+-----------+-------+------+------+--------------+ | 'CHROM' | 'POS' | 'ID' | 'REF' | 'ALT' | 'QUAL' | 'FILTER' | 'SAMPLE' | 'GT' | 'GQ' | 'DP' | 'HQ' | +=========+=======+=============+=======+=======+========+==========+===========+=======+======+======+==============+ | '19' | 111 | None | 'A' | [C] | 9.6 | [] | 'NA00001' | '0|0' | None | None | [10, 10] | +---------+-------+-------------+-------+-------+--------+----------+-----------+-------+------+------+--------------+ | '19' | 111 | None | 'A' | [C] | 9.6 | [] | 'NA00002' | '0|0' | None | None | [10, 10] | +---------+-------+-------------+-------+-------+--------+----------+-----------+-------+------+------+--------------+ | '19' | 111 | None | 'A' | [C] | 9.6 | [] | 'NA00003' | '0/1' | None | None | [3, 3] | +---------+-------+-------------+-------+-------+--------+----------+-----------+-------+------+------+--------------+ | '19' | 112 | None | 'A' | [G] | 10 | [] | 'NA00001' | '0|0' | None | None | [10, 10] | +---------+-------+-------------+-------+-------+--------+----------+-----------+-------+------+------+--------------+ | '19' | 112 | None | 'A' | [G] | 10 | [] | 'NA00002' | '0|0' | None | None | [10, 10] | +---------+-------+-------------+-------+-------+--------+----------+-----------+-------+------+------+--------------+ | '19' | 112 | None | 'A' | [G] | 10 | [] | 'NA00003' | '0/1' | None | None | [3, 3] | +---------+-------+-------------+-------+-------+--------+----------+-----------+-------+------+------+--------------+ | '20' | 14370 | 'rs6054257' | 'G' | [A] | 29 | [] | 'NA00001' | '0|0' | 48 | 1 | [51, 51] | +---------+-------+-------------+-------+-------+--------+----------+-----------+-------+------+------+--------------+ | '20' | 14370 | 'rs6054257' | 'G' | [A] | 29 | [] | 'NA00002' | '1|0' | 48 | 8 | [51, 51] | +---------+-------+-------------+-------+-------+--------+----------+-----------+-------+------+------+--------------+ | '20' | 14370 | 'rs6054257' | 'G' | [A] | 29 | [] | 'NA00003' | '1/1' | 43 | 5 | [None, None] | +---------+-------+-------------+-------+-------+--------+----------+-----------+-------+------+------+--------------+ | '20' | 17330 | None | 'T' | [A] | 3 | ['q10'] | 'NA00001' | '0|0' | 49 | 3 | [58, 50] | +---------+-------+-------------+-------+-------+--------+----------+-----------+-------+------+------+--------------+
New in version 0.5.