[9b26b7]: / deepvariant / vcf_candidate_importer.py

Download this file

77 lines (68 with data), 2.9 kB

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
# Copyright 2019 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its
# contributors may be used to endorse or promote products derived from this
# software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""A VcfCandidateImporter producing DeepVariantCall and gVCF records.
This module provides a way to call variants with a proposed VCF that contains
candidates to consider.
"""
from typing import Dict, List
from deepvariant import variant_caller
from deepvariant.protos import deepvariant_pb2
from deepvariant.python import allelecounter
from third_party.nucleus.io import vcf
class VcfCandidateImporter(variant_caller.VariantCaller):
"""Call variants and gvcf records from a VCF."""
def __init__(
self,
options,
candidates_vcf,
use_cache_table=True,
max_cache_coverage=100,
):
super(VcfCandidateImporter, self).__init__(
options=options,
use_cache_table=use_cache_table,
max_cache_coverage=max_cache_coverage,
)
self.vcf_reader = vcf.NativeVcfReader(candidates_vcf).c_reader
def get_candidates(
self,
allele_counters: Dict[str, allelecounter.AlleleCounter],
sample_name: str,
) -> List[deepvariant_pb2.DeepVariantCall]:
return self.cpp_variant_caller_from_vcf.calls_from_vcf(
allele_counters[sample_name], self.vcf_reader
)
def get_candidate_positions(
self,
allele_counters: Dict[str, allelecounter.AlleleCounter],
sample_name: str,
):
return self.cpp_variant_caller_from_vcf.call_positions_from_vcf(
allele_counters[sample_name], self.vcf_reader
)