changeset 0:962b0366a980 draft

Uploaded

Binary file BAMtoIDX.jar has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_scidx.py	Tue Nov 24 08:13:56 2015 -0500
@@ -0,0 +1,69 @@
+"""
+bam_to_scidx.py
+
+Input: BAM file
+Output: Converted scidx file
+"""
+import optparse
+import os
+import shutil
+import subprocess
+import sys
+import tempfile
+
+BUFF_SIZE = 1048576
+
+
+def get_stderr_exception(tmp_err, tmp_stderr):
+    """
+    Return a stderr string of reasonable size.
+    """
+    tmp_stderr.close()
+    # Get stderr, allowing for case where it's very large.
+    tmp_stderr = open(tmp_err, 'rb')
+    stderr_str = ''
+    buffsize = BUFF_SIZE
+    try:
+        while True:
+            stderr_str += tmp_stderr.read(buffsize)
+            if not stderr_str or len(stderr_str) % buffsize != 0:
+                break
+    except OverflowError:
+        pass
+    tmp_stderr.close()
+    return stderr_str
+
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit(1)
+
+
+parser = optparse.OptionParser()
+parser.add_option('-j', '--jar_file', dest='jar_file', type='string', help='BAMtoIDX.jar')
+parser.add_option('-b', '--input_bam', dest='input_bam', type='string', help='Input dataset in BAM format')
+parser.add_option('-i', '--input_bai', dest='input_bai', type='string', help='Input dataset index')
+parser.add_option('-r', '--read', dest='read', type='int', default=0, help='Reads.')
+parser.add_option('-o', '--output', dest='output', type='string', help='Output dataset in scidx format')
+options, args = parser.parse_args()
+
+tmp_dir = tempfile.mkdtemp(prefix='tmp-scidx-')
+tmp_out = tempfile.NamedTemporaryFile().name
+tmp_stdout = open(tmp_out, 'wb')
+tmp_err = tempfile.NamedTemporaryFile().name
+tmp_stderr = open(tmp_err, 'wb')
+
+# Link input BAM file and associated index file into the working directory.
+input_data_file_name = "input.bam"
+os.link(options.input_bam, os.path.join(tmp_dir, input_data_file_name))
+os.link(options.input_bai, os.path.join(tmp_dir, "%s.bai" % input_data_file_name))
+
+cmd = "java -jar %s -b %s -s %d -o %s" % (options.jar_file, input_data_file_name, options.read, options.output)
+proc = subprocess.Popen(args=cmd, stdout=tmp_stdout, stderr=tmp_stderr, shell=True, cwd=tmp_dir)
+return_code = proc.wait()
+if return_code != 0:
+    error_message = get_stderr_exception(tmp_err, tmp_stderr)
+    stop_err(error_message)
+
+if tmp_dir and os.path.exists(tmp_dir):
+    shutil.rmtree(tmp_dir)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_scidx.xml	Tue Nov 24 08:13:56 2015 -0500
@@ -0,0 +1,50 @@
+<tool id="bam_to_scidx" name="Convert BAM to ScIdx" version="1.0.0">
+    <description></description>
+    <command>
+        <![CDATA[
+            python $__tool_directory__/bam_to_scidx.py
+            -j $__tool_directory__/BAMtoIDX.jar
+            -b "$input_bam"
+            -i "${input_bam.metadata.bam_index}"
+            -r $read
+            -o "$output"
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_bam" type="data" format="bam" label="BAM file" help="BAM file must be sorted and indexed" />
+        <param name="read" type="select" label="Read to output">
+            <option value="0" selected="True">Read1</option>
+            <option value="1">Read2</option>
+            <option value="2">Combined</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="scidx" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="input.bam" ftype="bam" />
+            <param name="read" value="0" />
+            <output name="output" file="output.scidx" />
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by
+tools within the Chip-exo Galaxy flavor.  The Chip-exo Galaxy flavor is used by the Center for
+Eukaryotic Gene Regulation labs at The Pennsylvania State University.  ScIdx files are 1-based.
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{None,
+            author = {None},
+            title = {None},
+            year = {None},
+            eprint = {None},
+            url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
+        }</citation>
+    </citations>
+</tool>

Binary file test-data/input.bam has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.scidx	Tue Nov 24 08:13:56 2015 -0500
@@ -0,0 +1,21 @@
+#2015-11-23 20:18:56.51;input.bam;READ1
+chrom	index	forward	reverse	value
+chr17	1820100	0	1	1
+chr17	1849175	1	0	1
+chr17	2778159	0	1	1
+chr17	3205518	0	1	1
+chr17	12974350	1	0	1
+chr17	20624912	0	1	1
+chr17	27071176	0	1	1
+chr17	34920819	1	0	1
+chr17	39810583	0	1	1
+chr17	43542379	0	1	1
+chr17	45800656	1	0	1
+chr17	47124830	0	1	1
+chr17	48697995	0	1	1
+chr17	54474619	0	1	1
+chr17	64901353	0	1	1
+chr17	69072332	1	0	1
+chr17	76184543	1	0	1
+chr17	76518878	0	1	1
+chr17	76941015	1	0	1