27031497878

Committed 05 Jun 2026 06:01PM UTC coverage: 82.563% (-0.04%) from 82.606%

Build # 27031497878

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #1406 from griffithlab/normalized_percentiles

More missing normalized percentile argument hookups

Coverage Stats

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

5 existing lines in 5 files now uncovered.

9517 of 11527 relevant lines covered (82.56%)

0.83 hits per line

Source File
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91.89

/pvactools/tools/valid_algorithms.py

import sys
import argparse

from pvactools.lib.prediction_class import *

def define_parser():
    parser = argparse.ArgumentParser(
        "pvactools valid_algorithms",
        description="Show a list of algorithms supported given the specified species and/or allele",
        formatter_class=argparse.ArgumentDefaultsHelpFormatter
    )
    parser.add_argument(
        "-a", "--allele",
        help="Show valid algorithms for the selected allele. "
             + "For a list of available alleles, use: `pvactools valid_alleles`.",
    )
    parser.add_argument(
        "-s", "--species",
        choices=sorted(set(list(PredictionClass.allele_to_species_map().values())), key=str.casefold),
        help="Show valid algorithms for the selected species only",
    )
    return parser

def main(args_input = sys.argv[1:]):
    parser = define_parser()
    args = parser.parse_args(args_input)

    if args.allele is None:
        valid_algorithms = []
        if args.species is None:
            valid_algorithms = PredictionClass.prediction_methods()
        else:
            prediction_algorithms = PredictionClass.prediction_methods()
            for algorithm in prediction_algorithms:
                cls = globals()[algorithm]
                alleles = cls().valid_allele_names()
                for allele in alleles:
                    if cls.species_for_allele(allele) == args.species:
                        valid_algorithms.append(algorithm)
                        break
    else:
        PredictionClass.check_alleles_valid([args.allele])
        if (args.species != None and PredictionClass.species_for_allele(args.allele) != args.species):
            raise Exception("Given species does not match given allele.")
            return
        valid_algorithms = []
        prediction_algorithms = PredictionClass.prediction_methods()
        for algorithm in prediction_algorithms:
            cls = globals()[algorithm]
            alleles = cls().valid_allele_names()
            if (args.allele in alleles) \
                  and (PredictionClass.species_for_allele(args.allele) == args.species \
                       or args.species == None):
                valid_algorithms.append(algorithm)
    print('\n'.join([a for a in valid_algorithms]))

if __name__ == "__main__":
    main()

1	import sys	1✔
2	import argparse	1✔
3
4	from pvactools.lib.prediction_class import *	1✔
5
6	def define_parser():	1✔
7	parser = argparse.ArgumentParser(	1✔
8	"pvactools valid_algorithms",
9	description="Show a list of algorithms supported given the specified species and/or allele",
10	formatter_class=argparse.ArgumentDefaultsHelpFormatter
11	)
12	parser.add_argument(	1✔
13	"-a", "--allele",
14	help="Show valid algorithms for the selected allele. "
15	+ "For a list of available alleles, use: `pvactools valid_alleles`.",
16	)
17	parser.add_argument(	1✔
18	"-s", "--species",
19	choices=sorted(set(list(PredictionClass.allele_to_species_map().values())), key=str.casefold),
20	help="Show valid algorithms for the selected species only",
21	)
22	return parser	1✔
23
24	def main(args_input = sys.argv[1:]):	1✔
25	parser = define_parser()	1✔
26	args = parser.parse_args(args_input)	1✔
27
28	if args.allele is None:	1✔
29	valid_algorithms = []	1✔
30	if args.species is None:	1✔
31	valid_algorithms = PredictionClass.prediction_methods()	×
32	else:
33	prediction_algorithms = PredictionClass.prediction_methods()	1✔
34	for algorithm in prediction_algorithms:	1✔
35	cls = globals()[algorithm]	1✔
36	alleles = cls().valid_allele_names()	1✔
37	for allele in alleles:	1✔
38	if cls.species_for_allele(allele) == args.species:	1✔
39	valid_algorithms.append(algorithm)	1✔
40	break	1✔
41	else:
42	PredictionClass.check_alleles_valid([args.allele])	1✔
43	if (args.species != None and PredictionClass.species_for_allele(args.allele) != args.species):	1✔
44	raise Exception("Given species does not match given allele.")	1✔
UNCOV 45	return	×
46	valid_algorithms = []	1✔
47	prediction_algorithms = PredictionClass.prediction_methods()	1✔
48	for algorithm in prediction_algorithms:	1✔
49	cls = globals()[algorithm]	1✔
50	alleles = cls().valid_allele_names()	1✔
51	if (args.allele in alleles) \	1✔
52	and (PredictionClass.species_for_allele(args.allele) == args.species \
53	or args.species == None):
54	valid_algorithms.append(algorithm)	1✔
55	print('\n'.join([a for a in valid_algorithms]))	1✔
56
57	if __name__ == "__main__":	1✔
58	main()	×

griffithlab / pVACtools / 27031497878

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