Mercurial > repos > yufei-luo > s_mart
diff SMART/DiffExpAnal/countNumber_parallel.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/DiffExpAnal/countNumber_parallel.py Mon Apr 29 03:20:15 2013 -0400 @@ -0,0 +1,96 @@ +#! /usr/bin/env python + + +import optparse, os, sys, subprocess, tempfile, shutil, tarfile, random +from optparse import OptionParser + +def stop_err(msg): + sys.stderr.write('%s\n' % msg) + sys.exit() + +def toTar(tarFileName, outCountNames): + dir = os.path.dirname(tarFileName) + tfile = tarfile.open(tarFileName + ".tmp.tar", "w") + currentPath = os.getcwd() + os.chdir(dir) + for file in outCountNames: + relativeFileName = os.path.basename(file) + tfile.add(relativeFileName) + os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName)) + tfile.close() + os.chdir(currentPath) + + +def __main__(): + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option("-i", "--input", dest="inputFile", help="input txt file, a list of overlapping results files.") + parser.add_option("-o", "--output", dest="outputFile", help="Out txt file.") + parser.add_option("-t", "--tar", dest="outputTar", default=None, help="output all count results in a tar file.") + (options, args) = parser.parse_args() + + #Parse the input txt file and read a list of transcripts files. + file = open(options.inputFile, "r") + lines = file.readlines() + inputFileNames = [] + outCountNames = [] + outputName = options.outputFile + resDirName = os.path.dirname(outputName) + '/' + + #Write output txt file and define all output count file names + out = open(outputName, "w") + out.write("label\tfiles\tgroup\n") + for line in lines: + tab = line.split() + inputFileNames.append(tab[1]) + outCountName = resDirName + tab[0] + "_outCount_%s.csv" % random.randrange(0, 10000) + outCountNames.append(outCountName) + out.write(tab[0] + '\t' + outCountName + '\t' + tab[0][5] + '\n') + file.close() + out.close() + + #Construct the lines commands + cmds = [] + for i in range(len(inputFileNames)): + cmd = "perl %s/SMART/DiffExpAnal/countNumber.pl " % os.environ["REPET_PATH"] + opts = "%s %s " % (inputFileNames[i], outCountNames[i]) + cmd += opts + cmds.append(cmd) + + tmp_files = [] + for i in range(len(cmds)): + try: + tmp_out = tempfile.NamedTemporaryFile().name + tmp_files.append(tmp_out) + tmp_stdout = open(tmp_out, 'wb') + tmp_err = tempfile.NamedTemporaryFile().name + tmp_files.append(tmp_err) + tmp_stderr = open(tmp_err, 'wb') + proc = subprocess.Popen(args=cmds[i], shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr) + returncode = proc.wait() + tmp_stderr.close() + #get stderr, allowing for case where it's very large + tmp_stderr = open(tmp_err, 'rb') + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read(buffsize) + if not stderr or len(stderr) % buffsize != 0: + break + except OverflowError: + pass + tmp_stdout.close() + tmp_stderr.close() + if returncode != 0: + raise Exception, stderr + except Exception, e: + stop_err('Error in :\n' + str(e)) + + if options.outputTar != None: + toTar(options.outputTar, outCountNames) + + for tmp_file in tmp_files: + os.remove(tmp_file) + +if __name__=="__main__":__main__()