18349595495

Committed 08 Oct 2025 03:20PM UTC coverage: 83.425% (-0.04%) from 83.46%

Build # 18349595495

Build Type

Pull #1309

github

Committed by

web-flow

Commit Message

Merge 07e9136fc into 9aa720e9d

Pull Request Pull Request #1309: Update --top-score-metric2 parameter help text for clarity and remove unnecessary usage

Run Details

6 of 6 new or added lines in 6 files covered. (100.0%)

87 existing lines in 9 files now uncovered.

8989 of 10775 relevant lines covered (83.42%)

0.83 hits per line

Source File
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97.37

/pvactools/lib/valid_algorithms.py

import sys
import argparse

from pvactools.lib.prediction_class import *

class ValidAlgorithms:
    def __init__(self, allele, species):
        self.allele = allele
        self.species = species

    def print_valid_algorithms(self):
        if self.allele is None:
            valid_algorithms = []
            if self.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) == self.species:
                            valid_algorithms.append(algorithm)
                            break
        else:
            PredictionClass.check_alleles_valid([self.allele])
            if (self.species != None and PredictionClass.species_for_allele(self.allele) != self.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 (self.allele in alleles) \
                      and (PredictionClass.species_for_allele(self.allele) == self.species \
                           or self.species == None):
                    valid_algorithms.append(algorithm)
        print('\n'.join([a for a in valid_algorithms]))

    @classmethod
    def parser(cls, tool="pvacseq"):
        parser = argparse.ArgumentParser(
            "%s valid_algorithms" % tool,
            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: `{} valid_alleles`.".format(tool),
        )
        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

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

griffithlab / pVACtools / 18349595495

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