Mercurial > repos > triasteran > bam_to_bigwig

comparison BamToBigWig_planemo/bam_to_bigwig_py3.py @ 2:447324f08654 draft

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author triasteran
date Tue, 22 Feb 2022 16:14:23 +0000
parents 012dc1867dc7
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1 #!/usr/bin/env python
2 #Original version copyright Brad Chapman with revisions from Peter Cock
3 #and ideas from Lance Parsons
4 """Convert BAM files to BigWig file format in a specified region.
5
6 Usage:
7 bam_to_wiggle.py <BAM file> [<YAML config>] [--outfile=<output file name>]
8
9 The optional config file (not used by the Galaxy interface) is in YAML format
10 and specifies the location of the binary tools.
11
12 program:
13 bedtools_genomeCoverageBed: genomeCoverageBed
14 ucsc_bedGraphToBigWig: bedGraphToBigWig
15
16 If not specified, these will be assumed to be present in the system path.
17
18 The script requires:
19 pysam (http://code.google.com/p/pysam/)
20 genomeCoverageBed from BedTools (http://code.google.com/p/bedtools/)
21 bedGraphToBigWig from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
22 If a configuration file is used, then PyYAML is also required (http://pyyaml.org/)
23 """
24 import os
25 import sys
26 import subprocess
27 import tempfile
28 from optparse import OptionParser
29 from contextlib import contextmanager, closing
30
31 import pysam
32
33 def main(bam_file, config_file=None, outfile=None, split=False):
34 if config_file:
35 import yaml
36 with open(config_file) as in_handle:
37 config = yaml.load(in_handle)
38 else:
39 config = {"program": {"ucsc_bedGraphToBigWig" : "bedGraphToBigWig",
40 "bedtools_genomeCoverageBed" : "genomeCoverageBed"}}
41 if outfile is None:
42 outfile = "%s.bigwig" % os.path.splitext(bam_file)[0]
43 if os.path.abspath(bam_file) == os.path.abspath(outfile):
44 sys.stderr.write("Bad arguments, input and output files are the same.\n")
45 sys.exit(1)
46 if os.path.exists(outfile) and os.path.getsize(outfile) > 0:
47 sys.stderr.write("Warning, output file already exists.\n")
48
49 sizes = get_sizes(bam_file, config)
50 #print ("Have %i references" % len(sizes))
51 if not sizes:
52 sys.stderr.write("Problem reading BAM header.\n")
53 sys.exit(1)
54
55 #Use a temp file to avoid any possiblity of not having write permission
56 temp_handle = tempfile.NamedTemporaryFile(delete=False)
57 temp_file = temp_handle.name
58 with closing(temp_handle):
59 print ("Calculating coverage...")
60 convert_to_graph(bam_file, split, config, temp_handle)
61 try:
62 print ("Converting %i MB graph file to bigwig..." % (os.path.getsize(temp_file) // (1024*1024)))
63 #Can't pipe this as stdin due to converter design,
64 #https://lists.soe.ucsc.edu/pipermail/genome/2011-March/025455.html
65 convert_to_bigwig(temp_file, sizes, config, outfile)
66 finally:
67 if os.path.isfile(temp_file):
68 os.remove(temp_file)
69 print ("Done")
70
71 @contextmanager
72 def indexed_bam(bam_file, config):
73 if not os.path.exists(bam_file + ".bai"):
74 pysam.index(bam_file)
75 sam_reader = pysam.Samfile(bam_file, "rb")
76 yield sam_reader
77 sam_reader.close()
78
79 def get_sizes(bam_file, config):
80 with indexed_bam(bam_file, config) as work_bam:
81 sizes = zip(work_bam.references, work_bam.lengths)
82 return sizes
83
84 def convert_to_graph(bam_file, split, config, out_handle):
85 cl = [config["program"]["bedtools_genomeCoverageBed"], "-ibam", bam_file, "-bg"]
86 if split:
87 cl.append("-split")
88 subprocess.check_call(cl, stdout=out_handle)
89
90 def convert_to_bigwig(bedgraph_file, chr_sizes, config, bw_file):
91 #This will be fine under Galaxy, but could use temp folder?
92 size_file = "%s-sizes.txt" % (os.path.splitext(bw_file)[0])
93 with open(size_file, "w") as out_handle:
94 for chrom, size in chr_sizes:
95 out_handle.write("%s\t%s\n" % (chrom, size))
96 try:
97 cl = [config["program"]["ucsc_bedGraphToBigWig"], bedgraph_file, size_file, bw_file]
98 subprocess.check_call(cl)
99 finally:
100 os.remove(size_file)
101 return bw_file
102
103 if __name__ == "__main__":
104 parser = OptionParser()
105 parser.add_option("-o", "--outfile", dest="outfile")
106 parser.add_option("-s", "--split", action="store_true", dest="split")
107 (options, args) = parser.parse_args()
108 if len(args) not in [1, 2]:
109 print ("Incorrect arguments")
110 print (__doc__)
111 sys.exit()
112 kwargs = dict(
113 outfile=options.outfile,
114 split=options.split)
115 main(*args, **kwargs)