changeset 4:14e5258d1b39

v0.1.1: Add the forgotten --split argument in XML and moves to using the new bedtools. Thanks to David Leader

--- a/bam_to_bigwig/README.txt	Wed Sep 05 21:19:42 2012 -0400
+++ b/bam_to_bigwig/README.txt	Tue Feb 11 15:55:22 2014 -0500
@@ -7,6 +7,9 @@
 History
 -------
 
+v0.1.1 passes the forgotten split argument and moves to using the new
+sub-command enabled bedtools. Thanks to David Leader.
+
 As of v0.1.0, the Galaxy tools uses a revised bam_to_bigwig.py script using
 genomeCoverageBed and bedGraphToBigWig - this approach allows gaps/skpis to
 be excluded from the coverage calculation, which is important for RNA-Seq.

--- a/bam_to_bigwig/bam_to_bigwig.py	Wed Sep 05 21:19:42 2012 -0400
+++ b/bam_to_bigwig/bam_to_bigwig.py	Tue Feb 11 15:55:22 2014 -0500
@@ -4,22 +4,14 @@
 """Convert BAM files to BigWig file format in a specified region.
 
 Usage:
-    bam_to_wiggle.py <BAM file> [<YAML config>] [--outfile=<output file name>]
-
-The optional config file (not used by the Galaxy interface) is in YAML format
-and specifies the location of the binary tools.
+    bam_to_wiggle.py <BAM file> [--outfile=<output file name>] [--split]
 
-program:
-  bedtools_genomeCoverageBed: genomeCoverageBed
-  ucsc_bedGraphToBigWig: bedGraphToBigWig
-
-If not specified, these will be assumed to be present in the system path.
+The --split argument is passed to bedtools genomecov
 
 The script requires:
     pysam (http://code.google.com/p/pysam/)
-    genomeCoverageBed from BedTools (http://code.google.com/p/bedtools/)
+    bedtools genomecov (http://code.google.com/p/bedtools/)
     bedGraphToBigWig from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
-If a configuration file is used, then PyYAML is also required (http://pyyaml.org/)
 """
 import os
 import sys
@@ -30,14 +22,9 @@
 
 import pysam
 
-def main(bam_file, config_file=None, outfile=None, split=False):
-    if config_file:
-        import yaml
-        with open(config_file) as in_handle:
-            config = yaml.load(in_handle)
-    else:
-        config = {"program": {"ucsc_bedGraphToBigWig" : "bedGraphToBigWig",
-                              "bedtools_genomeCoverageBed" : "genomeCoverageBed"}}
+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):
@@ -59,7 +46,7 @@
         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))
+        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)
@@ -82,7 +69,7 @@
     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)
@@ -94,7 +81,7 @@
         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)

--- a/bam_to_bigwig/bam_to_bigwig.xml	Wed Sep 05 21:19:42 2012 -0400
+++ b/bam_to_bigwig/bam_to_bigwig.xml	Tue Feb 11 15:55:22 2014 -0500
@@ -1,6 +1,6 @@
-<tool id="bam_to_bigwig" name="BAM to BigWig" version="0.1.0">
+<tool id="bam_to_bigwig" name="BAM to BigWig" version="0.1.1">
   <description>Calculates coverage from a BAM alignment file</description>
-  <command interpreter="python">bam_to_bigwig.py $align --outfile=$out</command>
+  <command interpreter="python">bam_to_bigwig.py $align --outfile=$out --split</command>
   <inputs>
     <param format="bam" name="align" type="data" label="BAM alignment file"/>
   </inputs>