Mercurial > repos > iuc > concoct

annotate coverage_table.py @ 2:7a145c72d375 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 77dea70f156d56c83b6851b61dc997d2b344bdc9
author iuc
date Fri, 01 Jul 2022 14:14:44 +0000
parents 031f84cb2fd3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
1 #!/usr/bin/env python
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
2
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
3 import argparse
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
4 import gzip
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
5 from functools import partial
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
6
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
7 from Bio import SeqIO
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
8
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
9
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
10 def generate_coverage_table(input_fasta, input_tabular, gzipped, output):
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
11 # Read input file into a dict and return everything
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
12 # in the table format required by CONCOCT.
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
13 gc_and_len_dict = get_gc_and_len_dict(input_fasta, gzipped)
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
14 assert(len(gc_and_len_dict) > 0)
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
15 bed_coverage_dict = get_bed_coverage_dict(input_tabular)
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
16
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
17 with open(output, 'w') as fh:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
18 # Output the header.
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
19 fh.write("contig\tlength")
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
20 t = tuple(range(len(bed_coverage_dict)))
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
21 fh.write("\tcov_mean_sample_%d\n" % len(t))
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
22 # Output the content.
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
23 for acc in gc_and_len_dict:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
24 # Fasta stats.
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
25 fh.write("%s\t%s" % (acc, gc_and_len_dict[acc]['length']))
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
26 # Mean
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
27 try:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
28 # Coverage mean
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
29 fh.write("\t%f" % (bed_coverage_dict[acc]["cov_mean"]))
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
30 except KeyError:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
31 # No reads mapped to this contig
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
32 fh.write("\t0")
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
33 fh.write("\n")
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
34
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
35
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
36 def get_bed_coverage_dict(input_tabular):
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
37 # Ddetermine mean coverage and percentage covered
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
38 # for each contig, returning a dict with fasta id
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
39 # as key and percentage covered and cov_mean as keys
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
40 # for the inner dict.
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
41 out_dict = {}
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
42
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
43 with open(input_tabular, 'r') as fh:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
44 for line in fh:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
45 line = line.rstrip('\r\n')
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
46 cols = line.split('\t')
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
47 try:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
48 d = out_dict[cols[0]]
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
49 except KeyError:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
50 d = {}
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
51 out_dict[cols[0]] = d
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
52 if int(cols[1]) == 0:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
53 d["percentage_covered"] = 100 - float(cols[4]) * 100.0
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
54 else:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
55 d["cov_mean"] = d.get("cov_mean", 0) + int(cols[1]) * float(cols[4])
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
56 return out_dict
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
57
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
58
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
59 def get_gc_and_len_dict(input_fasta, gzipped):
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
60 # Creates a dictionary with the fasta id as key
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
61 # and GC and length as keys for the inner dictionary.
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
62 if gzipped:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
63 _open = partial(gzip.open, mode='rt')
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
64 else:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
65 _open = open
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
66
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
67 out_dict = {}
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
68 with _open(input_fasta) as input_fh:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
69 for rec in SeqIO.parse(input_fh, "fasta"):
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
70 out_dict[rec.id] = {}
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
71 out_dict[rec.id]["length"] = len(rec.seq)
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
72 return out_dict
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
73
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
74
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
75 parser = argparse.ArgumentParser(description=__doc__)
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
76 parser.add_argument('--input_tabular', action='store', dest='input_tabular', help='bedtools genomeCoverageBed bed file')
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
77 parser.add_argument('--input_fasta', action='store', dest='input_fasta', help='Contigs fasta file')
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
78 parser.add_argument("--gzipped", action="store_true", dest="gzipped", default=False, help="input_fasta is gzipped")
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
79 parser.add_argument('--output', action='store', dest='output', help='Output file')
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
80
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
81 args = parser.parse_args()
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
82
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
parents:
diff changeset
83 generate_coverage_table(args.input_fasta, args.input_tabular, args.gzipped, args.output)