| Previous changeset 4:14e5258d1b39 (2014-02-11) Next changeset 6:9163e1db4c16 (2016-05-12) |
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Commit message:
Fix issues with setting up subprocess call. Thanks to David Leader |
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modified:
bam_to_bigwig/bam_to_bigwig.py |
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| diff -r 14e5258d1b39 -r 52bcd04ee0d6 bam_to_bigwig/bam_to_bigwig.py --- a/bam_to_bigwig/bam_to_bigwig.py Tue Feb 11 15:55:22 2014 -0500 +++ b/bam_to_bigwig/bam_to_bigwig.py Mon Feb 24 10:02:20 2014 -0500 |
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| @@ -1,10 +1,11 @@ #!/usr/bin/env python -#Original version copyright Brad Chapman with revisions from Peter Cock -#and ideas from Lance Parsons """Convert BAM files to BigWig file format in a specified region. +Original version copyright Brad Chapman with revisions from Peter Cock +and ideas from Lance Parsons + Usage: - bam_to_wiggle.py <BAM file> [--outfile=<output file name>] [--split] + bam_to_bigwig.py <BAM file> [--outfile=<output file name>] [--split] The --split argument is passed to bedtools genomecov @@ -69,7 +70,7 @@ return sizes def convert_to_graph(bam_file, split, config, out_handle): - cl = [config["program"]["bedtools_genomeCoverageBed"]] + ["-ibam", bam_file, "-bg"] + cl = config["program"]["bedtools_genomeCoverageBed"] + ["-ibam", bam_file, "-bg"] if split: cl.append("-split") subprocess.check_call(cl, stdout=out_handle) @@ -81,7 +82,7 @@ for chrom, size in chr_sizes: out_handle.write("%s\t%s\n" % (chrom, size)) try: - cl = [config["program"]["ucsc_bedGraphToBigWig"]] + [bedgraph_file, size_file, bw_file] + cl = config["program"]["ucsc_bedGraphToBigWig"] + [bedgraph_file, size_file, bw_file] subprocess.check_call(cl) finally: os.remove(size_file) |