-
Notifications
You must be signed in to change notification settings - Fork 0
/
validate.py
120 lines (88 loc) · 4.7 KB
/
validate.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
#!/usr/bin/env python3
import argparse
import compare
import os
import utilities
import validators
def arguments():
docs = {'description': 'A script for validating the output of fngr.py',
'epilog': 'Output is returned in JSON format to stdout'}
parser = argparse.ArgumentParser(**docs)
data = parser.add_argument_group(title='Data',
description='Input FASTA files')
data.add_argument('--ingroup', nargs='+', type=utilities.fasta,
metavar='FASTAs', required=True,
help='FASTA file(s) belonging to the target species')
data.add_argument('--outgroup', nargs='+', type=utilities.fasta,
metavar='FASTAs', required=True,
help='FASTA file(s) serving as the source \
of foreign sequence to the ingroup')
parms = parser.add_argument_group(title='Analysis Parameters',
description='')
parms.add_argument('--organism', type=str.lower,
metavar='TAXONOMY', required=True,
help='Taxonomic name of target species')
parms.add_argument('--foreign', type=str.lower, metavar='TAXONOMY',
required=True, help='Taxonomic name of outgroup')
parms.add_argument('--contig-mean', type=float, metavar='NUM',
required=True, help='Mean size of synthetic contigs')
parms.add_argument('--contig-stdev', type=float,
metavar='NUM', required=True,
help='Standard deviation in synthetic contig lengths')
parms.add_argument('--insertion-mean', type=float,
metavar='NUM', required=True,
help='Mean length of foreign sequence insertions')
parms.add_argument('--insertion-stdev', type=float,
metavar='NUM', required=True,
help='Standard deviation in foreign \
sequence insertions')
parms.add_argument('--iterations', type=int, metavar='INT', default=10,
help='Iterations of each test to perform [10]')
parms.add_argument('--fragment', type=int, metavar='INT', default=250,
help='Pseudoread size (bp) into which Fngr divides \
assemblies for kraken [250]')
parms.add_argument('--threshold', type=int, metavar='INT', default=100,
help='Number of consecutive reads required to \
call a sequence foreign [100]')
resources = parser.add_argument_group(title='Resources',
description='External resources \
used by Fngr')
resources.add_argument('--fngr', required=True, metavar='PATH',
help='Path to fngr.py')
resources.add_argument('--kraken-database', required=True, metavar='PATH',
help='Path to Kraken database')
resources.add_argument('--nt-database', default=None, metavar='PATH',
help='Path to NCBI `nt` database')
resources.add_argument('--cores', type=int, default=None, metavar='INT',
help='Number of CPU cores to use [all]')
return parser.parse_args()
def main():
args = arguments()
fngr = utilities.Fngr(prog=args.fngr, organism=args.organism,
fragment=args.fragment, threshold=args.threshold,
kraken_db=args.kraken_database,
nt_db=args.nt_database,
cores=args.cores)
results = validators.validate(sources=args.outgroup,
recipients=args.ingroup,
gene_mean=args.insertion_mean,
gene_stdev=args.insertion_stdev,
contig_mean=args.contig_mean,
contig_stdev=args.contig_stdev,
iterations=args.iterations,
fngr=fngr)
utilities.user_msg('')
expected = {result: compare.create_expected(results[result], args.foreign)
for result in results}
fngr_output = {res: [r.result for r in results[res]] for res in results}
comparisons = compare.compare_each_genome(expected, fngr_output)
import pprint
pp = pprint.PrettyPrinter(indent =2)
for i in comparisons:
pp.pprint(i)
pp.pprint(comparisons[i])
print('')
metacomparison = compare.metacompare(comparisons)
pp.pprint(metacomparison)
if __name__ == '__main__':
main()