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