9781104697

Committed 03 Jul 2024 03:56PM UTC coverage: 88.33% (-6.4%) from 94.753%

Build Type

github

Committed by kodysy02

Commit Message

Defaulting convert_ucsc_contig_names to True for consistency with past behavior

Pull Request Pull Request #253: Defaulting convert_ucsc_contig_names to True for consistency with past behavior

Run Details

1 of 1 new or added line in 1 file covered. (100.0%)

144 existing lines in 17 files now uncovered.

1544 of 1748 relevant lines covered (88.33%)

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75.0

/varcode/cli/variant_args.py

# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

from argparse import ArgumentParser

from ..vcf import load_vcf
from ..maf import load_maf
from ..variant_collection import VariantCollection
from ..variant import Variant


def add_variant_args(arg_parser):
    """
    Extends an ArgumentParser instance with the following commandline arguments:
        --vcf
        --genome
        --maf
        --variant
        --json-variants
    """
    variant_arg_group = arg_parser.add_argument_group(
        title="Variants",
        description="Genomic variant files")

    variant_arg_group.add_argument(
        "--vcf",
        default=[],
        action="append",
        help="Genomic variants in VCF format")

    variant_arg_group.add_argument(
        "--maf",
        default=[],
        action="append",
        help="Genomic variants in TCGA's MAF format",)

    variant_arg_group.add_argument(
        "--variant",
        default=[],
        action="append",
        nargs=4,
        metavar=("CHR", "POS", "REF", "ALT"),
        help=(
            "Individual variant as 4 arguments giving chromsome, position, ref,"
            " and alt. Example: chr1 3848 C G. Use '.' to indicate empty alleles"
            " for insertions or deletions."))

    variant_arg_group.add_argument(
        "--genome",
        type=str,
        help=(
            "What reference assembly your variant coordinates are using. "
            "Examples: 'hg19', 'GRCh38', or 'mm9'. "
            "This argument is ignored for MAF files, since each row includes "
            "the reference. "
            "For VCF files, this is used if specified, and otherwise is guessed from "
            "the header. For variants specfied on the commandline with --variant, "
            "this option is required."))

    variant_arg_group.add_argument(
        "--download-reference-genome-data",
        action="store_true",
        default=False,
        help=(
            ("Automatically download genome reference data required for "
             "annotation using PyEnsembl. Otherwise you must first run "
             "'pyensembl install' for the release/species corresponding "
             "to the genome used in your VCF.")))

    variant_arg_group.add_argument(
        "--json-variants",
        default=[],
        action="append",
        help="Path to Varcode.VariantCollection object serialized as a JSON file.")

    return variant_arg_group


def make_variants_parser(**kwargs):
    """
    Parameters
    ----------
    **kwargs : dict
        Passed directly to argparse.ArgumentParser

    Creates argparse.ArgumentParser instance with options needed for loading
    variants from VCF, MAF, or JSON files.
    """
    parser = ArgumentParser(**kwargs)
    add_variant_args(parser)
    return parser


def download_and_install_reference_data(variant_collections):
    unique_genomes = {
        variant.ensembl
        for variant_collection in variant_collections
        for variant in variant_collection
    }
    for genome in unique_genomes:
        if not genome.required_local_files_exist():
            genome.download()
            genome.index()


def variant_collection_from_args(args, required=True):
    variant_collections = []

    for vcf_path in args.vcf:
        variant_collections.append(
            load_vcf(vcf_path, genome=args.genome))

    for maf_path in args.maf:
        variant_collections.append(load_maf(maf_path))

    if args.variant:
        if not args.genome:
            raise ValueError(
                "--genome must be specified when using --variant")

        variants = [
            Variant(
                chromosome,
                start=position,
                ref=ref,
                alt=alt,
                genome=args.genome)
            for (chromosome, position, ref, alt)
            in args.variant
        ]
        variant_collection = VariantCollection(variants)
        variant_collections.append(variant_collection)

    for json_path in args.json_variants:
        with open(json_path, 'r') as f:
            variant_collections.append(
                VariantCollection.from_json(f.read()))

    if required and len(variant_collections) == 0:
        raise ValueError(
            "No variants loaded (use --maf, --vcf, --variant, or --json-variants options)")

    if args.download_reference_genome_data:
        download_and_install_reference_data(variant_collections)

    # pylint: disable=no-value-for-parameter
    return VariantCollection.union(*variant_collections)

1	# Licensed under the Apache License, Version 2.0 (the "License");
2	# you may not use this file except in compliance with the License.
3	# You may obtain a copy of the License at
4	#
5	# http://www.apache.org/licenses/LICENSE-2.0
6	#
7	# Unless required by applicable law or agreed to in writing, software
8	# distributed under the License is distributed on an "AS IS" BASIS,
9	# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10	# See the License for the specific language governing permissions and
11	# limitations under the License.
12
13	from argparse import ArgumentParser	3✔
14
15	from ..vcf import load_vcf	3✔
16	from ..maf import load_maf	3✔
17	from ..variant_collection import VariantCollection	3✔
18	from ..variant import Variant	3✔
19
20
21	def add_variant_args(arg_parser):	3✔
22	"""
23	Extends an ArgumentParser instance with the following commandline arguments:
24	--vcf
25	--genome
26	--maf
27	--variant
28	--json-variants
29	"""
30	variant_arg_group = arg_parser.add_argument_group(	3✔
31	title="Variants",
32	description="Genomic variant files")
33
34	variant_arg_group.add_argument(	3✔
35	"--vcf",
36	default=[],
37	action="append",
38	help="Genomic variants in VCF format")
39
40	variant_arg_group.add_argument(	3✔
41	"--maf",
42	default=[],
43	action="append",
44	help="Genomic variants in TCGA's MAF format",)
45
46	variant_arg_group.add_argument(	3✔
47	"--variant",
48	default=[],
49	action="append",
50	nargs=4,
51	metavar=("CHR", "POS", "REF", "ALT"),
52	help=(
53	"Individual variant as 4 arguments giving chromsome, position, ref,"
54	" and alt. Example: chr1 3848 C G. Use '.' to indicate empty alleles"
55	" for insertions or deletions."))
56
57	variant_arg_group.add_argument(	3✔
58	"--genome",
59	type=str,
60	help=(
61	"What reference assembly your variant coordinates are using. "
62	"Examples: 'hg19', 'GRCh38', or 'mm9'. "
63	"This argument is ignored for MAF files, since each row includes "
64	"the reference. "
65	"For VCF files, this is used if specified, and otherwise is guessed from "
66	"the header. For variants specfied on the commandline with --variant, "
67	"this option is required."))
68
69	variant_arg_group.add_argument(	3✔
70	"--download-reference-genome-data",
71	action="store_true",
72	default=False,
73	help=(
74	("Automatically download genome reference data required for "
75	"annotation using PyEnsembl. Otherwise you must first run "
76	"'pyensembl install' for the release/species corresponding "
77	"to the genome used in your VCF.")))
78
79	variant_arg_group.add_argument(	3✔
80	"--json-variants",
81	default=[],
82	action="append",
83	help="Path to Varcode.VariantCollection object serialized as a JSON file.")
84
85	return variant_arg_group	3✔
86
87
88	def make_variants_parser(**kwargs):	3✔
89	"""
90	Parameters
91	----------
92	**kwargs : dict
93	Passed directly to argparse.ArgumentParser
94
95	Creates argparse.ArgumentParser instance with options needed for loading
96	variants from VCF, MAF, or JSON files.
97	"""
98	parser = ArgumentParser(**kwargs)	3✔
99	add_variant_args(parser)	3✔
100	return parser	3✔
101
102
103	def download_and_install_reference_data(variant_collections):	3✔
UNCOV 104	unique_genomes = {	×
105	variant.ensembl
106	for variant_collection in variant_collections
107	for variant in variant_collection
108	}
109	for genome in unique_genomes:	×
110	if not genome.required_local_files_exist():	×
111	genome.download()	×
112	genome.index()	×
113
114
115	def variant_collection_from_args(args, required=True):	3✔
116	variant_collections = []	3✔
117
118	for vcf_path in args.vcf:	3✔
UNCOV 119	variant_collections.append(	×
120	load_vcf(vcf_path, genome=args.genome))
121
122	for maf_path in args.maf:	3✔
123	variant_collections.append(load_maf(maf_path))	3✔
124
125	if args.variant:	3✔
126	if not args.genome:	3✔
UNCOV 127	raise ValueError(	×
128	"--genome must be specified when using --variant")
129
130	variants = [	3✔
131	Variant(
132	chromosome,
133	start=position,
134	ref=ref,
135	alt=alt,
136	genome=args.genome)
137	for (chromosome, position, ref, alt)
138	in args.variant
139	]
140	variant_collection = VariantCollection(variants)	3✔
141	variant_collections.append(variant_collection)	3✔
142
143	for json_path in args.json_variants:	3✔
144	with open(json_path, 'r') as f:	×
UNCOV 145	variant_collections.append(	×
146	VariantCollection.from_json(f.read()))
147
148	if required and len(variant_collections) == 0:	3✔
UNCOV 149	raise ValueError(	×
150	"No variants loaded (use --maf, --vcf, --variant, or --json-variants options)")
151
152	if args.download_reference_genome_data:	3✔
153	download_and_install_reference_data(variant_collections)	×
154
155	# pylint: disable=no-value-for-parameter
156	return VariantCollection.union(*variant_collections)	3✔

openvax / varcode / 9781104697

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