25186739369

Committed 30 Apr 2026 08:05PM UTC coverage: 89.171% (+0.3%) from 88.876%

Build # 25186739369

Build Type

push

github

Committed by

web-flow

Commit Message

Improve CLI validation errors (#147)

Coverage Stats

22 of 24 new or added lines in 3 files covered. (91.67%)

3829 of 4294 relevant lines covered (89.17%)

2.68 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

77.78

/topiary/cli/script.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.

"""
Script to generate epitope predictions from somatic cancer variants
and (optionally) tumor RNA-seq data.

Example usage:
    topiary \
        --mhc-predictor netmhcpan
        --mhc-alleles-file HLA.txt
        --vcf somatic.vcf
        --rna-gene-fpkm-file genes.fpkm_tracking
        --rna-transcript-fpkm-file isoforms.fpkm_tracking
        --filter-ic50 500
        --filter-percentile 2
        --output results.csv
"""

import sys

import argcomplete

from .args import arg_parser, predict_epitopes_from_args

from .outputs import write_outputs


def parse_args(args_list=None):
    if args_list is None:
        args_list = sys.argv[1:]
    argcomplete.autocomplete(arg_parser)
    return arg_parser.parse_args(args_list)


def main(args_list=None):
    """
    Script entry-point to predict neo-epitopes from genomic variants using
    Topiary.
    """
    args = parse_args(args_list)
    try:
        df = predict_epitopes_from_args(args)
    except (OSError, ValueError) as e:
        arg_parser.error(str(e))
    write_outputs(df, args)
    print("Total count: %d" % len(df))
    return 0

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	"""
14	Script to generate epitope predictions from somatic cancer variants
15	and (optionally) tumor RNA-seq data.
16
17	Example usage:
18	topiary \
19	--mhc-predictor netmhcpan
20	--mhc-alleles-file HLA.txt
21	--vcf somatic.vcf
22	--rna-gene-fpkm-file genes.fpkm_tracking
23	--rna-transcript-fpkm-file isoforms.fpkm_tracking
24	--filter-ic50 500
25	--filter-percentile 2
26	--output results.csv
27	"""
28
29	import sys	3✔
30
31	import argcomplete	3✔
32
33	from .args import arg_parser, predict_epitopes_from_args	3✔
34
35	from .outputs import write_outputs	3✔
36
37
38	def parse_args(args_list=None):	3✔
39	if args_list is None:	3✔
40	args_list = sys.argv[1:]	×
41	argcomplete.autocomplete(arg_parser)	3✔
42	return arg_parser.parse_args(args_list)	3✔
43
44
45	def main(args_list=None):	3✔
46	"""
47	Script entry-point to predict neo-epitopes from genomic variants using
48	Topiary.
49	"""
50	args = parse_args(args_list)	3✔
51	try:	3✔
52	df = predict_epitopes_from_args(args)	3✔
53	except (OSError, ValueError) as e:	3✔
54	arg_parser.error(str(e))	3✔
55	write_outputs(df, args)	×
56	print("Total count: %d" % len(df))	×
NEW 57	return 0	×

openvax / topiary / 25186739369

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous