changeset 11:14c34615b202 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwameth_wrapper.py	Wed Sep 14 04:53:27 2016 -0400
@@ -0,0 +1,45 @@
+#!/usr/bin/env python
+import argparse
+import subprocess
+import os
+import shlex
+
+def createIndex(fname):
+    """
+    Create an index for a file, return where it is
+    """
+    d = os.mkdir("index_dir")
+    os.link(fname, "index_dir/genome.fa")
+    cmd = "{}/bwameth.py index {}/index_dir/genome.fa".format(os.path.dirname(__file__), os.getcwd())
+    proc = subprocess.Popen(args=shlex.split(cmd))
+    returncode = proc.wait()
+    if returncode != 0:
+        raise Exception("Error during '%s'" % cmd)
+    return "{}/index_dir/genome.fa".format(os.getcwd())
+
+
+parser = argparse.ArgumentParser(description="A wrapper around bwameth for Galaxy. There's minimal argument checking done")
+parser.add_argument('-p', '--numThreads', type=int, default=4, help="number of threads")
+parser.add_argument('--makeIndex', help="Given a fasta file, index it")
+parser.add_argument('--premadeIndex', help="If an index already exists, this is the fasta file associated with it (the index files must be in the same directory")
+parser.add_argument('--readGroup', help="The read group text, if desired")
+parser.add_argument('files', nargs="+", help="Fasta files (possibly gzipped, if the file names end in .gz)")
+args = parser.parse_args()
+
+if args.makeIndex:
+    ifile = createIndex(args.makeIndex)
+else:
+    ifile = args.premadeIndex
+
+files = " ".join(['{}'.format(x) for x in args.files])
+if args.readGroup:
+    files = "{} --read-group '{}'".format(files, args.readGroup)
+
+cmd = "{}/bwameth.py -t {} --reference '{}' {} | samtools view -u - | samtools sort -@ {} - output".format(os.path.dirname(__file__), args.numThreads, ifile, files, args.numThreads)
+of = open("temp.sh", "w")
+of.write("{}\n".format(cmd))
+of.close()
+try:
+    subprocess.check_call(["bash", "./temp.sh"])
+except:
+    raise Exception("Error during '%s'" % cmd)