1532

pending completion

Build # 1532

Build Type

Pull #545

travis-ci

Committed by

web-flow

Commit Message

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Pull Request Pull Request #545: Handle mhcflurry 1.6.0 renamed output headers

Run Details

17 of 17 new or added lines in 5 files covered. (100.0%)

3898 of 4627 relevant lines covered (84.24%)

2.53 hits per line

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79.07

/tools/pvacseq/main.py

import argparse
import sys
from subprocess import call
import os
import pkg_resources
from tools.pvacseq import *

def define_parser():
    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
    subparsers = parser.add_subparsers()

    #add subcommands
    run_main_program_parser = subparsers.add_parser(
        "run",
        help="Runs the pVACseq pipeline",
        add_help=False
    )
    run_main_program_parser.set_defaults(func=run)

    binding_filter_parser = subparsers.add_parser(
        "binding_filter",
        help="Filters variants processed by IEDB by binding score",
        add_help=False
    )
    binding_filter_parser.set_defaults(func=binding_filter)

    coverage_filter_parser = subparsers.add_parser(
        "coverage_filter",
        help="Filters variants processed by IEDB by coverage, vaf, and gene expression",
        add_help=False
    )
    coverage_filter_parser.set_defaults(func=coverage_filter)

    transcript_support_level_filter_parser = subparsers.add_parser(
        "transcript_support_level_filter",
        help="Filters variants processed by IEDB by transcript support level",
        add_help=False
    )
    transcript_support_level_filter_parser.set_defaults(func=transcript_support_level_filter)

    top_score_filter_parser = subparsers.add_parser(
        "top_score_filter",
        help="Pick the best neoepitope for each variant",
        add_help=False,
    )
    top_score_filter_parser.set_defaults(func=top_score_filter)

    generate_protein_fasta_parser = subparsers.add_parser(
        "generate_protein_fasta",
        help="Generate an annotated fasta file from a VCF with protein sequences of mutations and matching wildtypes",
        add_help=False
    )
    generate_protein_fasta_parser.set_defaults(func=generate_protein_fasta)

    generate_condensed_ranked_report_parser = subparsers.add_parser(
        "generate_condensed_ranked_report",
        help="Generate a condensed, ranked report from a pVACseq .all_epitopes.tsv or .filtered.tsv report file.",
        add_help=False
    )
    generate_condensed_ranked_report_parser.set_defaults(func=generate_condensed_ranked_report)

    download_example_data_parser = subparsers.add_parser(
        "download_example_data",
        help="Downloads example input and output files",
        add_help=False
    )
    download_example_data_parser.set_defaults(func=download_example_data)

    install_vep_plugin_parser = subparsers.add_parser(
        "install_vep_plugin",
        help="Installs the Wildtype VEP plugin into your VEP_plugins directory",
        add_help=False
    )
    install_vep_plugin_parser.set_defaults(func=install_vep_plugin)

    valid_alleles_parser = subparsers.add_parser(
        "valid_alleles",
        help="Shows a list of valid allele names",
        add_help=False
    )
    valid_alleles_parser.set_defaults(func=valid_alleles)

    allele_specific_cutoffs_parser = subparsers.add_parser(
        "allele_specific_cutoffs",
        help="Show the allele specific cutoffs",
        add_help=False,
    )
    allele_specific_cutoffs_parser.set_defaults(func=allele_specific_cutoffs)
    return parser

def main():
    parser = define_parser()
    args = parser.parse_known_args()
    try:
        args[0].func.main(args[1])
    except AttributeError as e:
        parser.print_help()
        print("Error: No command specified")
        raise


if __name__ == '__main__':
    main()

1	import argparse	3✔
2	import sys	3✔
3	from subprocess import call	3✔
4	import os	3✔
5	import pkg_resources	3✔
6	from tools.pvacseq import *	3✔
7
8	def define_parser():	3✔
9	parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)	3✔
10	subparsers = parser.add_subparsers()	3✔
11
12	#add subcommands
13	run_main_program_parser = subparsers.add_parser(	3✔
14	"run",
15	help="Runs the pVACseq pipeline",
16	add_help=False
17	)
18	run_main_program_parser.set_defaults(func=run)	3✔
19
20	binding_filter_parser = subparsers.add_parser(	3✔
21	"binding_filter",
22	help="Filters variants processed by IEDB by binding score",
23	add_help=False
24	)
25	binding_filter_parser.set_defaults(func=binding_filter)	3✔
26
27	coverage_filter_parser = subparsers.add_parser(	3✔
28	"coverage_filter",
29	help="Filters variants processed by IEDB by coverage, vaf, and gene expression",
30	add_help=False
31	)
32	coverage_filter_parser.set_defaults(func=coverage_filter)	3✔
33
34	transcript_support_level_filter_parser = subparsers.add_parser(	3✔
35	"transcript_support_level_filter",
36	help="Filters variants processed by IEDB by transcript support level",
37	add_help=False
38	)
39	transcript_support_level_filter_parser.set_defaults(func=transcript_support_level_filter)	3✔
40
41	top_score_filter_parser = subparsers.add_parser(	3✔
42	"top_score_filter",
43	help="Pick the best neoepitope for each variant",
44	add_help=False,
45	)
46	top_score_filter_parser.set_defaults(func=top_score_filter)	3✔
47
48	generate_protein_fasta_parser = subparsers.add_parser(	3✔
49	"generate_protein_fasta",
50	help="Generate an annotated fasta file from a VCF with protein sequences of mutations and matching wildtypes",
51	add_help=False
52	)
53	generate_protein_fasta_parser.set_defaults(func=generate_protein_fasta)	3✔
54
55	generate_condensed_ranked_report_parser = subparsers.add_parser(	3✔
56	"generate_condensed_ranked_report",
57	help="Generate a condensed, ranked report from a pVACseq .all_epitopes.tsv or .filtered.tsv report file.",
58	add_help=False
59	)
60	generate_condensed_ranked_report_parser.set_defaults(func=generate_condensed_ranked_report)	3✔
61
62	download_example_data_parser = subparsers.add_parser(	3✔
63	"download_example_data",
64	help="Downloads example input and output files",
65	add_help=False
66	)
67	download_example_data_parser.set_defaults(func=download_example_data)	3✔
68
69	install_vep_plugin_parser = subparsers.add_parser(	3✔
70	"install_vep_plugin",
71	help="Installs the Wildtype VEP plugin into your VEP_plugins directory",
72	add_help=False
73	)
74	install_vep_plugin_parser.set_defaults(func=install_vep_plugin)	3✔
75
76	valid_alleles_parser = subparsers.add_parser(	3✔
77	"valid_alleles",
78	help="Shows a list of valid allele names",
79	add_help=False
80	)
81	valid_alleles_parser.set_defaults(func=valid_alleles)	3✔
82
83	allele_specific_cutoffs_parser = subparsers.add_parser(	3✔
84	"allele_specific_cutoffs",
85	help="Show the allele specific cutoffs",
86	add_help=False,
87	)
88	allele_specific_cutoffs_parser.set_defaults(func=allele_specific_cutoffs)	3✔
89	return parser	3✔
90
91	def main():	3✔
92	parser = define_parser()	×
93	args = parser.parse_known_args()	×
94	try:	×
95	args[0].func.main(args[1])	×
96	except AttributeError as e:	×
97	parser.print_help()	×
98	print("Error: No command specified")	×
99	raise	×
100
101
102	if __name__ == '__main__':	3✔
103	main()	×

griffithlab / pVACtools / 1532

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