def vcfunpackinfo(table, *keys):
"""
Unpack the INFO field into separate fields. E.g.::
>>> import petl as etl
>>> # activate bio extensions
... import petlx.bio
>>> table1 = (
... etl
... .fromvcf('fixture/sample.vcf', samples=None)
... .vcfunpackinfo()
... )
>>> table1
+-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+
| CHROM | POS | ID | REF | ALT | QUAL | FILTER | AA | AC | AF | AN | DB | DP | H2 | NS |
+=======+=========+=============+=====+========+======+=========+======+======+================+======+======+======+======+======+
| '19' | 111 | None | 'A' | [C] | 9.6 | None | None | None | None | None | None | None | None | None |
+-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+
| '19' | 112 | None | 'A' | [G] | 10 | None | None | None | None | None | None | None | None | None |
+-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+
| '20' | 14370 | 'rs6054257' | 'G' | [A] | 29 | [] | None | None | [0.5] | None | True | 14 | True | 3 |
+-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+
| '20' | 17330 | None | 'T' | [A] | 3 | ['q10'] | None | None | [0.017] | None | None | 11 | None | 3 |
+-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+
| '20' | 1110696 | 'rs6040355' | 'A' | [G, T] | 67 | [] | 'T' | None | [0.333, 0.667] | None | True | 10 | None | 2 |
+-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+
...
"""
result = etl.unpackdict(table, 'INFO', keys=keys)
return result
def vcfunpackinfo(table, *keys):
"""
Unpack the INFO field into separate fields. E.g.::
>>> import petl as etl
>>> # activate bio extensions
... import petlx.bio
>>> table1 = (
... etl
... .fromvcf('fixture/sample.vcf', samples=None)
... .vcfunpackinfo()
... )
>>> table1
+-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+
| CHROM | POS | ID | REF | ALT | QUAL | FILTER | AA | AC | AF | AN | DB | DP | H2 | NS |
+=======+=========+=============+=====+========+======+=========+======+======+================+======+======+======+======+======+
| '19' | 111 | None | 'A' | [C] | 9.6 | None | None | None | None | None | None | None | None | None |
+-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+
| '19' | 112 | None | 'A' | [G] | 10 | None | None | None | None | None | None | None | None | None |
+-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+
| '20' | 14370 | 'rs6054257' | 'G' | [A] | 29 | [] | None | None | [0.5] | None | True | 14 | True | 3 |
+-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+
| '20' | 17330 | None | 'T' | [A] | 3 | ['q10'] | None | None | [0.017] | None | None | 11 | None | 3 |
+-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+
| '20' | 1110696 | 'rs6040355' | 'A' | [G, T] | 67 | [] | 'T' | None | [0.333, 0.667] | None | True | 10 | None | 2 |
+-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+
...
"""
result = etl.unpackdict(table, 'INFO', keys=keys)
return result
def unpackcall(tbl, *keys, **kwargs):
"""
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] |
+---------+-------+-------------+-------+-------+--------+----------+-----------+-------+------+------+--------------+
.. versionadded:: 0.5
"""
if not keys:
if hasattr(tbl, 'filename'):
try:
import vcf as pyvcf
except ImportError as e:
raise UnsatisfiedDependency(e, dep_message)
reader = pyvcf.Reader(filename=tbl.filename)
# all FORMAT
keys = reader.formats.keys()
else:
tbl = convert(tbl, 'CALL', lambda v: v.data._asdict()
) # enable sampling of keys from data
result = unpackdict(tbl, 'CALL', keys=keys)
if 'prefix' in kwargs:
result = rename(result, {k: kwargs['prefix'] + k for k in keys})
if hasattr(tbl, 'filename'):
return VCFWrapper(result, tbl.filename)
else:
return result
def unpackcall(tbl, *keys, **kwargs):
"""
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] |
+---------+-------+-------------+-------+-------+--------+----------+-----------+-------+------+------+--------------+
.. versionadded:: 0.5
"""
if not keys:
if hasattr(tbl, 'filename'):
try:
import vcf as pyvcf
except ImportError as e:
raise UnsatisfiedDependency(e, dep_message)
reader = pyvcf.Reader(filename=tbl.filename)
# all FORMAT
keys = reader.formats.keys()
else:
tbl = convert(tbl, 'CALL', lambda v: v.data._asdict()) # enable sampling of keys from data
result = unpackdict(tbl, 'CALL', keys=keys)
if 'prefix' in kwargs:
result = rename(result, {k: kwargs['prefix'] + k for k in keys})
if hasattr(tbl, 'filename'):
return VCFWrapper(result, tbl.filename)
else:
return result
def unpack_dict(self,
column,
keys=None,
include_original=False,
sample_size=1000,
missing=None,
prepend=True,
prepend_value=None):
"""
Unpack dictionary values from one column into separate columns
`Args:`
column: str
The column name to unpack
keys: list
The dict keys in the column to unpack. If ``None`` will unpack
all.
include_original: boolean
Retain original column after unpacking
sample_size: int
Number of rows to sample before determining columns
missing: str
If a value is missing, the value to fill it with
prepend:
Prepend the column name of the unpacked values. Useful for
avoiding duplicate column names
prepend_value:
Value to prepend new columns if ``prepend=True``. If None, will
set to column name.
"""
if prepend:
if prepend_value is None:
prepend_value = column
self.table = petl.convert(
self.table, column,
lambda v: self._prepend_dict(v, prepend_value))
self.table = petl.unpackdict(self.table,
column,
keys=keys,
includeoriginal=include_original,
samplesize=sample_size,
missing=missing)
return self
# time consumed retrieving rows from t2
c2.time
# actual time consumed by the convert step
c2.time - c1.time
# unpackdict
table1 = (('foo', 'bar'),
(1, {'baz': 'a', 'quux': 'b'}),
(2, {'baz': 'c', 'quux': 'd'}),
(3, {'baz': 'e', 'quux': 'f'}))
from petl import unpackdict, look
look(table1)
table2 = unpackdict(table1, 'bar')
look(table2)
# unique
table1 = (('foo', 'bar', 'baz'),
('A', 1, 2),
('B', '2', '3.4'),
('D', 'xyz', 9.0),
('B', u'3', u'7.8'),
('B', '2', 42),
('E', None, None),
('D', 4, 12.3),
('F', 7, 2.3))
from petl import unique, look
# time consumed retrieving rows from t2
c2.time
# actual time consumed by the convert step
c2.time - c1.time
# unpackdict
table1 = (('foo', 'bar'),
(1, {'baz': 'a', 'quux': 'b'}),
(2, {'baz': 'c', 'quux': 'd'}),
(3, {'baz': 'e', 'quux': 'f'}))
from petl import unpackdict, look
look(table1)
table2 = unpackdict(table1, 'bar')
look(table2)
# unique
table1 = (('foo', 'bar', 'baz'),
('A', 1, 2),
('B', '2', '3.4'),
('D', 'xyz', 9.0),
('B', u'3', u'7.8'),
('B', '2', 42),
('E', None, None),
('D', 4, 12.3),
('F', 7, 2.3))
from petl import unique, look
def unpackinfo(tbl, *keys, **kwargs):
"""
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 |
+---------+---------+-------------+-------+-----------+--------+----------+------+------+--------+------+----------------+------+------+------+
.. versionadded:: 0.5
"""
if not keys:
if hasattr(tbl, 'filename'):
try:
import vcf as pyvcf
except ImportError as e:
raise UnsatisfiedDependency(e, dep_message)
reader = pyvcf.Reader(filename=tbl.filename)
# all INFO
keys = reader.infos.keys()
result = unpackdict(tbl, 'INFO', keys=keys)
if 'prefix' in kwargs:
result = rename(result, {k: kwargs['prefix'] + k for k in keys})
if hasattr(tbl, 'filename'):
return VCFWrapper(result, tbl.filename)
else:
return result
key=('room_id'),
aggregation=aggregations)
external_ids = etl.fromdicts(
[{
'id': '3979',
'external_id': '95109151-af77-11e9-94fa-a860b6030e49'
}, {
'id': '3980',
'external_id': '95d8c92e-af77-11e9-99b7-a860b6030e49'
}, {
'id': '3982',
'external_id': '97163c4a-af77-11e9-bdf9-a860b6030e49'
}],
header=['id', 'external_id'])
aggregated_summary = etl.unpackdict(aggregated_summary,
'creation_data')
file_name = 'datasets-%s.csv' % datetime.now().strftime('%Y%m%d%H%M%S')
directory = 'csv'
if not os.path.exists(directory):
os.makedirs(directory)
# etl.tocsv(aggregated_summary, './%s/%s' % (directory, file_name))
# logging.info('This %s has been exported' % file_name)
rooms, participations = storing_data_preparation(aggregated_summary)
participations = etl.leftjoin(participations,
external_ids,
lkey='participant_id',
rkey='id',
rprefix='r_')
from __future__ import absolute_import, print_function, division
# unpack()
##########
import petl as etl
table1 = [['foo', 'bar'],
[1, ['a', 'b']],
[2, ['c', 'd']],
[3, ['e', 'f']]]
table2 = etl.unpack(table1, 'bar', ['baz', 'quux'])
table2
# unpackdict()
##############
import petl as etl
table1 = [['foo', 'bar'],
[1, {'baz': 'a', 'quux': 'b'}],
[2, {'baz': 'c', 'quux': 'd'}],
[3, {'baz': 'e', 'quux': 'f'}]]
table2 = etl.unpackdict(table1, 'bar')
table2
def unpackinfo(tbl, *keys, **kwargs):
"""
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 |
+---------+---------+-------------+-------+-----------+--------+----------+------+------+--------+------+----------------+------+------+------+
.. versionadded:: 0.5
"""
if not keys:
if hasattr(tbl, 'filename'):
try:
import vcf as pyvcf
except ImportError as e:
raise UnsatisfiedDependency(e, dep_message)
reader = pyvcf.Reader(filename=tbl.filename)
# all INFO
keys = reader.infos.keys()
result = unpackdict(tbl, 'INFO', keys=keys)
if 'prefix' in kwargs:
result = rename(result, {k: kwargs['prefix'] + k for k in keys})
if hasattr(tbl, 'filename'):
return VCFWrapper(result, tbl.filename)
else:
return result
