Mercurial > repos > nick > duplex

annotate utils/precheck.py @ 18:e4d75f9efb90 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
author nick
date Thu, 02 Feb 2017 18:44:31 -0500
parents af383638de66
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
1 #!/usr/bin/env python
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
2 from __future__ import division
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
3 import sys
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
4 import argparse
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
5 import getreads
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
6
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
7 OPT_DEFAULTS = {'tag_len':12, 'const_len':5, 'min_reads':3, 'human':True}
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
8 USAGE = "%(prog)s [options]"
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
9 DESCRIPTION = """Print statistics on the raw duplex sequencing reads."""
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
10 EPILOG = """Warning: This tracks all barcodes in a dict, so it can take a lot of memory. A guideline
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
11 is about 200 bytes per (12bp) tag. For example, it took about 800MB for a 10GB, 32 million read
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
12 dataset with an average of 4 pairs per barcode."""
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
13
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
14
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
15 def main(argv):
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
16
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
17 parser = argparse.ArgumentParser(description=DESCRIPTION, epilog=EPILOG)
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
18 parser.set_defaults(**OPT_DEFAULTS)
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
19
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
20 parser.add_argument('infile1', metavar='reads_1.fq',
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
21 help='The first mates in the read pairs.')
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
22 parser.add_argument('infile2', metavar='reads_2.fq',
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
23 help='The second mates in the read pairs.')
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
24 parser.add_argument('-t', '--tag-length', dest='tag_len', type=int)
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
25 parser.add_argument('-c', '--constant-length', dest='const_len', type=int)
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
26 parser.add_argument('-C', '--computer', dest='human', action='store_false',
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
27 help='Print results in computer-readable format. This will be a tab-delimited version of the '
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
28 'output, in the same order, but with two columns: stat name and value.')
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
29 parser.add_argument('-m', '--min-reads', type=int,
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
30 help='The minimum number of reads required in each single-stranded family. Default: '
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
31 '%(default)s')
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
32 parser.add_argument('-v', '--validate', action='store_true',
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
33 help='Check the id\'s of the reads to make sure the correct reads are mated into pairs (the '
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
34 'id\'s of mates must be identical).')
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
35
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
36 args = parser.parse_args(argv[1:])
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
37
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
38 with open(args.infile1) as infileh1:
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
39 with open(args.infile2) as infileh2:
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
40 barcodes = read_files(infileh1, infileh2, tag_len=args.tag_len, validate=args.validate)
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
41
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
42 stats = get_stats(barcodes, tag_len=args.tag_len, min_reads=args.min_reads)
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
43 print_stats(stats, min_reads=args.min_reads, human=args.human)
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
44
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
45
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
46 def read_files(infileh1, infileh2, tag_len=12, validate=False):
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
47 reader1 = getreads.getparser(infileh1, filetype='fastq').parser()
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
48 reader2 = getreads.getparser(infileh2, filetype='fastq').parser()
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
49 barcodes = {}
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
50 while True:
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
51 try:
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
52 read1 = reader1.next()
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
53 read2 = reader2.next()
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
54 except StopIteration:
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
55 break
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
56 if validate and read1.id != read2.id:
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
57 raise getreads.FormatError('Read pair mismatch: "{}" and "{}"'.format(read1.id, read2.id))
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
58 alpha = read1.seq[:tag_len]
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
59 beta = read2.seq[:tag_len]
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
60 barcode = alpha + beta
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
61 if barcode in barcodes:
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
62 barcodes[barcode] += 1
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
63 else:
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
64 barcodes[barcode] = 1
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
65 return barcodes
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
66
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
67
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
68 def get_stats(barcodes, tag_len=12, min_reads=3):
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
69 passed_sscs = 0
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
70 duplexes = 0
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
71 passed_duplexes = 0
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
72 singletons = 0
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
73 total_pairs = 0
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
74 for barcode, count in barcodes.items():
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
75 total_pairs += count
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
76 if count == 1:
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
77 singletons += 1
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
78 if count >= min_reads:
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
79 passed_sscs += 1
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
80 alpha = barcode[:tag_len]
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
81 beta = barcode[tag_len:]
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
82 reverse = beta + alpha
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
83 if reverse in barcodes:
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
84 duplexes += 1
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
85 if count >= min_reads and barcodes[reverse] >= min_reads:
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
86 passed_duplexes += 1
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
87 # Each full duplex ends up being counted twice. Halve it to get the real total.
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
88 stats = {
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
89 'pairs':total_pairs,
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
90 'barcodes':len(barcodes),
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
91 'avg_pairs':total_pairs/len(barcodes),
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
92 'singletons':singletons,
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
93 'duplexes':duplexes//2,
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
94 'passed_sscs':passed_sscs*2,
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
95 'passed_duplexes':passed_duplexes,
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
96 }
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
97 return stats
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
98
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
99
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
100 def print_stats(stats, min_reads=3, human=True):
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
101 all_stats = stats.copy()
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
102 all_stats.update({'min_reads':min_reads})
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
103 if human:
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
104 print """Total read pairs:\t{pairs}
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
105 Unique barcodes:\t{barcodes}
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
106 Avg # of read pairs per barcode:\t{avg_pairs}
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
107 Singletons:\t{singletons}
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
108 Barcodes with reverse (other strand) present:\t{duplexes}
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
109 Passing threshold of {min_reads} reads per single-strand consensus:
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
110 \tSingle-strand consensus sequences:\t{passed_sscs}
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
111 \tDuplex consensus sequences:\t{passed_duplexes}""".format(**all_stats)
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
112 else:
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
113 for stat in ('pairs', 'barcodes', 'avg_pairs', 'singletons', 'duplexes', 'min_reads',
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
114 'passed_sscs', 'passed_duplexes'):
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
115 print '{}\t{}'.format(stat, all_stats[stat])
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
116
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
117
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
118 def fail(message):
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
119 sys.stderr.write(message+"\n")
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
120 sys.exit(1)
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
121
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
122 if __name__ == '__main__':
af383638de66 planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
nick
parents:
diff changeset
123 sys.exit(main(sys.argv))