24167477073

Committed 09 Apr 2026 01:22AM UTC coverage: 86.166% (-0.4%) from 86.577%

Build # 24167477073

Build Type

push

github

Committed by

iskandr

Commit Message

Add tab completion support via argcomplete, bump to 4.3.2

Closes #7. Optional dependency: pip install 'topiary[completion]'.
Uses argcomplete.autocomplete() for bash/zsh/fish tab completion
of all CLI arguments.

Coverage Stats

1 of 7 new or added lines in 2 files covered. (14.29%)

2 existing lines in 1 file now uncovered.

1090 of 1265 relevant lines covered (86.17%)

2.58 hits per line

Source File
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0.0

/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

try:
    import argcomplete
except ImportError:
    argcomplete = None

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:]
    if argcomplete is not None:
        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)
    print("Topiary commandline arguments:")
    print(args)
    df = predict_epitopes_from_args(args)
    write_outputs(df, args)
    print("Total count: %d" % len(df))

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	×
30
NEW 31	try:	×
NEW 32	import argcomplete	×
NEW 33	except ImportError:	×
NEW 34	argcomplete = None	×
35
UNCOV 36	from .args import arg_parser, predict_epitopes_from_args	×
37
38	from .outputs import write_outputs	×
39
40
41	def parse_args(args_list=None):	×
42	if args_list is None:	×
43	args_list = sys.argv[1:]	×
NEW 44	if argcomplete is not None:	×
NEW 45	argcomplete.autocomplete(arg_parser)	×
UNCOV 46	return arg_parser.parse_args(args_list)	×
47
48
49	def main(args_list=None):	×
50	"""
51	Script entry-point to predict neo-epitopes from genomic variants using
52	Topiary.
53	"""
54	args = parse_args(args_list)	×
55	print("Topiary commandline arguments:")	×
56	print(args)	×
57	df = predict_epitopes_from_args(args)	×
58	write_outputs(df, args)	×
59	print("Total count: %d" % len(df))	×

openvax / topiary / 24167477073

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