diff smart_toolShed/SMART/Java/Python/WrappGetReadDistribution.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/WrappGetReadDistribution.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,58 @@
+#! /usr/bin/env python
+from optparse import OptionParser
+import tarfile
+import os
+import re
+import shutil
+import subprocess
+
+SMART_PATH = "%s/SMART" % os.environ["REPET_PATH"]
+
+def toTar(tarFileName, directory):
+    fileName = os.path.splitext(tarFileName)[0]
+    fileNameBaseName = os.path.basename(fileName)
+    tfile = tarfile.open(fileName + ".tmp.tar", "w")
+    list = os.listdir(directory)
+    for file in list:
+        if re.search(str(fileNameBaseName), file):
+            tfile.add(file)
+    os.system("mv %s %s" % (fileName + ".tmp.tar", options.outTarFileName))
+    tfile.close()
+    
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Get Read Distribution v1.0.1: Plot the number of identical reads and give the most represented. [Category: Visualization]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",     dest="inputFileName",  action="store",               type="string", help="input file sequence [compulsory] [format: file in sequence format given by -f]")
+    parser.add_option("-f", "--format",    dest="format",         action="store",               type="string", help="format of the file [compulsory] [format: sequence file format]")
+    parser.add_option("-n", "--number",    dest="number",         action="store", default=None, type="int",    help="keep the best n    [format: int]")
+    parser.add_option("-p", "--percent",   dest="percent",        action="store", default=None, type="float",  help="keep the best n\% [format: float]")
+    parser.add_option("-o", "--output",    dest="outTarFileName", action="store",               type="string", help="output file [compulsory] [format: zip]")
+
+    (options, args) = parser.parse_args()
+
+
+    absPath = os.getcwd()
+    print "the current path is :", absPath
+    directory = "/tmp/wrappGetReadDistribution"
+    print "the dir path is :", directory
+    if not os.path.exists(directory):
+        os.makedirs(directory)
+    os.chdir(directory)
+    if options.inputFileName != None and options.format != None and options.outTarFileName != None:
+        outputFileName = os.path.splitext(os.path.basename(options.outTarFileName))[0]
+        cmd = "python %s/Java/Python/getReadDistribution.py -i %s -f %s -o %s -D %s" % (SMART_PATH, options.inputFileName, options.format, outputFileName, directory)
+    if options.number != None :
+        cmd += " -n %s" % options.number
+    if options.percent != None :
+        cmd += " -p %s" % options.percent
+    print "cmd is: ", cmd    
+    status = subprocess.call(cmd, shell=True)
+    if status != 0:
+            raise Exception("Problem with the execution of command!")
+    toTar(options.outTarFileName, directory)
+    shutil.rmtree(directory)
+