Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data
view DiffExpAnal/countNumber_parallel.py @ 6:59cc55f611f6 draft
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author | yufei-luo |
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date | Tue, 22 Jan 2013 10:46:42 -0500 |
parents | 63799b789162 |
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#! /usr/bin/env python """ Yufei LUO """ 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 countNumber.pl " 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__()