Mercurial > repos > yufei-luo > s_mart
diff SMART/DiffExpAnal/bam_to_sam_parallel_unSQL.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/bam_to_sam_parallel_unSQL.py Mon Apr 29 03:20:15 2013 -0400 @@ -0,0 +1,145 @@ +#!/usr/bin/env python +""" +Converts BAM data to sorted SAM data. +usage: bam_to_sam.py [options] + --input1: SAM file to be converted + --output1: output dataset in bam format +""" + +import optparse, os, sys, subprocess, tempfile, shutil, tarfile, random +from commons.core.launcher.Launcher import Launcher +from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory +#from galaxy import eggs +#import pkg_resources; pkg_resources.require( "bx-python" ) +#from bx.cookbook import doc_optparse +#from galaxy import util + +def stop_err( msg ): + sys.stderr.write( '%s\n' % msg ) + sys.exit() + +def toTar(tarFileName, samOutputNames): + dir = os.path.dirname(tarFileName) + tfile = tarfile.open(tarFileName + ".tmp.tar", "w") + currentPath = os.getcwd() + os.chdir(dir) + for file in samOutputNames: + relativeFileName = os.path.basename(file) + tfile.add(relativeFileName) + os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName)) + tfile.close() + os.chdir(currentPath) + +def _map(iLauncher, cmd, cmdStart, cmdFinish ): + lCmds = [] + lCmds.extend(cmd) + lCmdStart = [] + lCmdStart.extend(cmdStart) + lCmdFinish = [] + lCmdFinish.extend(cmdFinish) + return(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish)) + +def _createSamToolsViewCmd(iLauncher, inputFile, tmp_sorted_aligns_file_name, header): + lArgs = [] + lArgs.append("-o %s" % inputFile) + lArgs.append("%s" % tmp_sorted_aligns_file_name) + if header: + lArgs.append("-h") + return iLauncher.getSystemCommand("samtools view", lArgs) + +def _createSamToolsSortCmd(iLauncher, inputFile, tmp_sorted_aligns_file_base): + lArgs = [] + lArgs.append("%s" % inputFile) + lArgs.append("%s" % tmp_sorted_aligns_file_base) + return iLauncher.getSystemCommand("samtools sort", lArgs) + +def __main__(): + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option('-t', '--tar', dest='outputTar', default=None, help='output all SAM results in a tar file.' ) + parser.add_option( '', '--input1', dest='input1', help='The input list of BAM datasets on txt format.' ) + #parser.add_option( '', '--input1', dest='input1', help='The input BAM dataset' ) + parser.add_option( '', '--output1', dest='output1', help='The output list of SAM datasets on txt format.' ) + #parser.add_option( '', '--output1', dest='output1', help='The output SAM dataset' ) + parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' ) + ( options, args ) = parser.parse_args() + + + #Parse the input txt file and read a list of BAM files. + file = open(options.input1, "r") + lines = file.readlines() + inputFileNames = [] + samOutputNames = [] + outputName = options.output1 + resDirName = os.path.dirname(outputName) + '/' + #Write output txt file and define all output sam file names. + out = open(outputName, "w") + for line in lines: + tab = line.split() + inputFileNames.append(tab[1]) + samOutName = resDirName + tab[0] + '_samOutput_%s.sam' % random.randrange(0, 10000) + samOutputNames.append(samOutName) + out.write(tab[0] + '\t' + samOutName + '\n') + file.close() + out.close() + + # output version # of tool + try: + tmp_files = [] + tmp = tempfile.NamedTemporaryFile().name + tmp_files.append(tmp) + tmp_stdout = open( tmp, 'wb' ) + proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout ) + tmp_stdout.close() + returncode = proc.wait() + stdout = None + for line in open( tmp_stdout.name, 'rb' ): + if line.lower().find( 'version' ) >= 0: + stdout = line.strip() + break + if stdout: + sys.stdout.write( 'Samtools %s\n' % stdout ) + else: + raise Exception + except: + sys.stdout.write( 'Could not determine Samtools version\n' ) + + tmp_dirs = [] + acronym = "bam_to_sam" + jobdb = TableJobAdaptatorFactory.createJobInstance() + iLauncher = Launcher(jobdb, os.getcwd(), "", "", os.getcwd(), os.getcwd(), "jobs", "", acronym, acronym, False, True) + lCmdsTuples = [] + for i in range(len(inputFileNames)): #Construct the lines commands + if os.path.getsize( inputFileNames[i] ) == 0: + raise Exception, 'Initial input txt file is empty.' + tmp_dir = tempfile.mkdtemp(dir="%s" % os.getcwd()) + tmp_dirs.append(tmp_dir) + tmp_sorted_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir ) + tmp_sorted_aligns_file_base = tmp_sorted_aligns_file.name + tmp_sorted_aligns_file_name = '%s.bam' % tmp_sorted_aligns_file.name + tmp_files.append(tmp_sorted_aligns_file_name) + tmp_sorted_aligns_file.close() + + inputFile = inputFileNames[i] + outputFile = samOutputNames[i] + cmd2Launch = [] + cmd2Launch.append(_createSamToolsSortCmd(iLauncher, inputFile, tmp_sorted_aligns_file_base)) + cmd2Launch.append(_createSamToolsViewCmd(iLauncher, outputFile, tmp_sorted_aligns_file_name, options.header)) + cmdStart = [] + cmdFinish = [] + lCmdsTuples.append(_map(iLauncher, cmd2Launch, cmdStart, cmdFinish)) + + iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, True) + + if options.outputTar != None: + toTar(options.outputTar, samOutputNames) + #clean up temp files + for tmp_dir in tmp_dirs: + if os.path.exists( tmp_dir ): + shutil.rmtree( tmp_dir ) + #print tmp_files + #for tmp in tmp_files: + # os.remove(tmp) + + +if __name__=="__main__": __main__()