diff bam_to_bigwig.py @ 6:9163e1db4c16 draft default tip

planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/bam_to_bigwig/ commit b5c3df21127fc27f66a97761173c07e161f2fa8e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_bigwig.py	Thu May 12 11:39:13 2016 -0400
@@ -0,0 +1,122 @@
+#!/usr/bin/env python
+"""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_bigwig.py <BAM file> [--outfile=<output file name>] [--split]
+
+The --split argument is passed to bedtools genomecov
+
+The script requires:
+    pysam (http://code.google.com/p/pysam/)
+    bedtools genomecov (http://code.google.com/p/bedtools/)
+    bedGraphToBigWig from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
+"""
+import os
+import sys
+import subprocess
+import tempfile
+from optparse import OptionParser
+from contextlib import contextmanager, closing
+
+import pysam
+
+
+def main(bam_file, outfile=None, split=False):
+    config = {"program": {"ucsc_bedGraphToBigWig": ["bedGraphToBigWig"],
+                          "bedtools_genomeCoverageBed":
+                          ["bedtools", "genomecov"]}}
+    if outfile is None:
+        outfile = "%s.bigwig" % os.path.splitext(bam_file)[0]
+    if os.path.abspath(bam_file) == os.path.abspath(outfile):
+        sys.stderr.write("Bad arguments, "
+                         "input and output files are the same.\n")
+        sys.exit(1)
+    if os.path.exists(outfile) and os.path.getsize(outfile) > 0:
+        sys.stderr.write("Warning, output file already exists.\n")
+
+    sizes = get_sizes(bam_file, config)
+    print "Have %i references" % len(sizes)
+    if not sizes:
+        sys.stderr.write("Problem reading BAM header.\n")
+        sys.exit(1)
+
+    # Use a temp file to avoid any possiblity of not having write permission
+    temp_handle = tempfile.NamedTemporaryFile(delete=False)
+    temp_file = temp_handle.name
+    with closing(temp_handle):
+        print "Calculating coverage..."
+        convert_to_graph(bam_file, split, config, temp_handle)
+    try:
+        print("Converting %i MB graph file to bigwig..." %
+              (os.path.getsize(temp_file) // (1024 * 1024)))
+        # Can't pipe this as stdin due to converter design,
+        # https://lists.soe.ucsc.edu/pipermail/genome/2011-March/025455.html
+        convert_to_bigwig(temp_file, sizes, config, outfile)
+    finally:
+        if os.path.isfile(temp_file):
+            os.remove(temp_file)
+    print "Done"
+
+
+@contextmanager
+def indexed_bam(bam_file, config):
+    if not os.path.exists(bam_file + ".bai"):
+        pysam.index(bam_file)
+    sam_reader = pysam.Samfile(bam_file, "rb")
+    yield sam_reader
+    sam_reader.close()
+
+
+def get_sizes(bam_file, config):
+    with indexed_bam(bam_file, config) as work_bam:
+        sizes = zip(work_bam.references, work_bam.lengths)
+    return sizes
+
+
+def convert_to_graph(bam_file, split, config, out_handle):
+    cl = config["program"]["bedtools_genomeCoverageBed"] + \
+        ["-ibam", bam_file, "-bg"]
+    if split:
+        cl.append("-split")
+    new_env = os.environ.copy()
+    new_env['LC_COLLATE'] = 'C'
+    p1 = subprocess.Popen(cl, stdout=subprocess.PIPE)
+    p2 = subprocess.Popen(["sort", "-k1,1", "-k2,2n"],
+                          env=new_env,
+                          stdin=p1.stdout,
+                          stdout=out_handle)
+    p1.stdout.close()
+    p2.communicate()
+
+
+def convert_to_bigwig(bedgraph_file, chr_sizes, config, bw_file):
+    # This will be fine under Galaxy, but could use temp folder?
+    size_file = "%s-sizes.txt" % (os.path.splitext(bw_file)[0])
+    with open(size_file, "w") as out_handle:
+        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]
+        subprocess.check_call(cl)
+    finally:
+        os.remove(size_file)
+    return bw_file
+
+
+if __name__ == "__main__":
+    parser = OptionParser()
+    parser.add_option("-o", "--outfile", dest="outfile")
+    parser.add_option("-s", "--split", action="store_true", dest="split")
+    (options, args) = parser.parse_args()
+    if len(args) not in [1, 2]:
+        print "Incorrect arguments"
+        print __doc__
+        sys.exit()
+    kwargs = dict(
+        outfile=options.outfile,
+        split=options.split)
+    main(*args, **kwargs)