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eff.py
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eff.py
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# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function, division
# standard library dependencies
import re
import logging
# internal dependencies
import vcfnp.config as config
logger = logging.getLogger(__name__)
debug = logger.debug
EFF_DEFAULT_DTYPE = [
('Effect', 'a33'),
('Effect_Impact', 'a8'),
('Functional_Class', 'a8'),
('Codon_Change', 'a7'), # N.B., will lose information for indels
('Amino_Acid_Change', 'a8'), # N.B., will lose information for indels
('Amino_Acid_Length', 'i4'),
('Gene_Name', 'a14'), # N.B., may be too short for some species
('Transcript_BioType', 'a20'),
('Gene_Coding', 'i1'),
('Transcript_ID', 'a20'),
('Exon', 'i1')
]
ANN_DEFAULT_DTYPE = [
('Allele', 'a12'),
('Annotation', 'a34'),
('Annotation_Impact', 'a8'),
('Gene_Name', 'a14'),
('Gene_ID', 'a14'),
('Feature_Type', 'a20'),
('Feature_ID', 'a14'),
('Transcript_BioType', 'a20'),
('Rank', 'i1'),
('HGVS_c', 'a12'),
('HGVS_p', 'a14'),
('cDNA_pos', 'i4'),
('cDNA_length', 'i4'),
('CDS_pos', 'i4'),
('CDS_length', 'i4'),
('AA_pos', 'i4'),
('AA_length', 'i4'),
('Distance', 'i4')
]
config.DEFAULT_INFO_DTYPE['EFF'] = EFF_DEFAULT_DTYPE
config.DEFAULT_VARIANT_ARITY['EFF'] = 1
config.DEFAULT_INFO_DTYPE['ANN'] = ANN_DEFAULT_DTYPE
config.DEFAULT_VARIANT_ARITY['ANN'] = 1
EFF_DEFAULT_FILLS = (b'.', b'.', b'.', b'.', b'.', -1, b'.', b'.', -1, b'.',
-1)
ANN_DEFAULT_FILLS = (b'.', b'.', b'.', b'.', b'.', b'.', b'.', b'.', -1, b'.',
b'.', -1, -1, -1, -1, -1, -1, -1)
_prog_eff_main = re.compile(b'([^(]+)\(([^)]+)\)')
def eff_default_transformer(fills=EFF_DEFAULT_FILLS):
"""
Return a simple transformer function for parsing EFF annotations. N.B.,
ignores all but the first effect.
"""
def _transformer(vals):
if len(vals) == 0:
return fills
else:
# ignore all but first effect
match_eff_main = _prog_eff_main.match(vals[0])
if match_eff_main is None:
logging.warning(
'match_eff_main is None: vals={}'.format(str(vals[0]))
)
return fills
eff = [match_eff_main.group(1)] \
+ match_eff_main.group(2).split(b'|')
result = tuple(
fill if v == b''
else int(v) if i == 5 or i == 10
else (1 if v == b'CODING' else 0) if i == 8
else v
for i, (v, fill) in enumerate(list(zip(eff, fills))[:11])
)
return result
return _transformer
def _ann_split2(b):
x, _, y = b.partition(b'/')
return [x, y]
def ann_default_transformer(fills=ANN_DEFAULT_FILLS):
"""
Return a simple transformer function for parsing ANN annotations. N.B.,
ignores all but the first effect.
"""
def _transformer(vals):
if len(vals) == 0:
return fills
else:
# ignore all but first effect
ann = vals[0].split(b'|')
ann = ann[:11] + _ann_split2(ann[11]) + _ann_split2(ann[12]) + \
_ann_split2(ann[13]) + ann[14:]
result = tuple(
fill if v == b''
else int(v.partition(b'/')[0]) if i == 8
else int(v) if 11 <= i < 18
else v
for i, (v, fill) in enumerate(list(zip(ann, fills))[:18])
)
return result
return _transformer
config.DEFAULT_TRANSFORMER['EFF'] = eff_default_transformer()
config.DEFAULT_TRANSFORMER['ANN'] = ann_default_transformer()
EFF_FIELDS = tuple(n for n, _ in EFF_DEFAULT_DTYPE)
# noinspection PyRedeclaration
ANN_FIELDS = tuple(n for n, _ in ANN_DEFAULT_DTYPE)
def flatten_eff(fill=b'.'):
def _flatten(vals):
if len(vals) == 0:
return [fill] * 11
else:
# ignore all but first effect
match_eff_main = _prog_eff_main.match(vals[0])
eff = [match_eff_main.group(1)] \
+ match_eff_main.group(2).split(b'|')
eff = [fill if v == b'' else v for v in eff[:11]]
return eff
return _flatten
def flatten_ann(fill=b'.'):
def _flatten(vals):
if len(vals) == 0:
return [fill] * 18
else:
# ignore all but first effect
ann = vals[0].split(b'|')
ann = ann[:11] + _ann_split2(ann[11]) + _ann_split2(ann[12]) + \
_ann_split2(ann[13]) + ann[14:]
ann = [fill if v == b'' else v for v in ann[:18]]
return ann
return _flatten
config.DEFAULT_FLATTEN['EFF'] = (EFF_FIELDS, flatten_eff)
config.DEFAULT_FLATTEN['ANN'] = (ANN_FIELDS, flatten_ann)