Mercurial > repos > yufei-luo > s_mart

comparison SMART/DiffExpAnal/bam_to_sam_parallel_unSQL.py @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 #!/usr/bin/env python
2 """
3 Converts BAM data to sorted SAM data.
4 usage: bam_to_sam.py [options]
5 --input1: SAM file to be converted
6 --output1: output dataset in bam format
7 """
8
9 import optparse, os, sys, subprocess, tempfile, shutil, tarfile, random
10 from commons.core.launcher.Launcher import Launcher
11 from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory
12 #from galaxy import eggs
13 #import pkg_resources; pkg_resources.require( "bx-python" )
14 #from bx.cookbook import doc_optparse
15 #from galaxy import util
16
17 def stop_err( msg ):
18 sys.stderr.write( '%s\n' % msg )
19 sys.exit()
20
21 def toTar(tarFileName, samOutputNames):
22 dir = os.path.dirname(tarFileName)
23 tfile = tarfile.open(tarFileName + ".tmp.tar", "w")
24 currentPath = os.getcwd()
25 os.chdir(dir)
26 for file in samOutputNames:
27 relativeFileName = os.path.basename(file)
28 tfile.add(relativeFileName)
29 os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName))
30 tfile.close()
31 os.chdir(currentPath)
32
33 def _map(iLauncher, cmd, cmdStart, cmdFinish ):
34 lCmds = []
35 lCmds.extend(cmd)
36 lCmdStart = []
37 lCmdStart.extend(cmdStart)
38 lCmdFinish = []
39 lCmdFinish.extend(cmdFinish)
40 return(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish))
41
42 def _createSamToolsViewCmd(iLauncher, inputFile, tmp_sorted_aligns_file_name, header):
43 lArgs = []
44 lArgs.append("-o %s" % inputFile)
45 lArgs.append("%s" % tmp_sorted_aligns_file_name)
46 if header:
47 lArgs.append("-h")
48 return iLauncher.getSystemCommand("samtools view", lArgs)
49
50 def _createSamToolsSortCmd(iLauncher, inputFile, tmp_sorted_aligns_file_base):
51 lArgs = []
52 lArgs.append("%s" % inputFile)
53 lArgs.append("%s" % tmp_sorted_aligns_file_base)
54 return iLauncher.getSystemCommand("samtools sort", lArgs)
55
56 def __main__():
57 #Parse Command Line
58 parser = optparse.OptionParser()
59 parser.add_option('-t', '--tar', dest='outputTar', default=None, help='output all SAM results in a tar file.' )
60 parser.add_option( '', '--input1', dest='input1', help='The input list of BAM datasets on txt format.' )
61 #parser.add_option( '', '--input1', dest='input1', help='The input BAM dataset' )
62 parser.add_option( '', '--output1', dest='output1', help='The output list of SAM datasets on txt format.' )
63 #parser.add_option( '', '--output1', dest='output1', help='The output SAM dataset' )
64 parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' )
65 ( options, args ) = parser.parse_args()
66
67
68 #Parse the input txt file and read a list of BAM files.
69 file = open(options.input1, "r")
70 lines = file.readlines()
71 inputFileNames = []
72 samOutputNames = []
73 outputName = options.output1
74 resDirName = os.path.dirname(outputName) + '/'
75 #Write output txt file and define all output sam file names.
76 out = open(outputName, "w")
77 for line in lines:
78 tab = line.split()
79 inputFileNames.append(tab[1])
80 samOutName = resDirName + tab[0] + '_samOutput_%s.sam' % random.randrange(0, 10000)
81 samOutputNames.append(samOutName)
82 out.write(tab[0] + '\t' + samOutName + '\n')
83 file.close()
84 out.close()
85
86 # output version # of tool
87 try:
88 tmp_files = []
89 tmp = tempfile.NamedTemporaryFile().name
90 tmp_files.append(tmp)
91 tmp_stdout = open( tmp, 'wb' )
92 proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout )
93 tmp_stdout.close()
94 returncode = proc.wait()
95 stdout = None
96 for line in open( tmp_stdout.name, 'rb' ):
97 if line.lower().find( 'version' ) >= 0:
98 stdout = line.strip()
99 break
100 if stdout:
101 sys.stdout.write( 'Samtools %s\n' % stdout )
102 else:
103 raise Exception
104 except:
105 sys.stdout.write( 'Could not determine Samtools version\n' )
106
107 tmp_dirs = []
108 acronym = "bam_to_sam"
109 jobdb = TableJobAdaptatorFactory.createJobInstance()
110 iLauncher = Launcher(jobdb, os.getcwd(), "", "", os.getcwd(), os.getcwd(), "jobs", "", acronym, acronym, False, True)
111 lCmdsTuples = []
112 for i in range(len(inputFileNames)): #Construct the lines commands
113 if os.path.getsize( inputFileNames[i] ) == 0:
114 raise Exception, 'Initial input txt file is empty.'
115 tmp_dir = tempfile.mkdtemp(dir="%s" % os.getcwd())
116 tmp_dirs.append(tmp_dir)
117 tmp_sorted_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
118 tmp_sorted_aligns_file_base = tmp_sorted_aligns_file.name
119 tmp_sorted_aligns_file_name = '%s.bam' % tmp_sorted_aligns_file.name
120 tmp_files.append(tmp_sorted_aligns_file_name)
121 tmp_sorted_aligns_file.close()
122
123 inputFile = inputFileNames[i]
124 outputFile = samOutputNames[i]
125 cmd2Launch = []
126 cmd2Launch.append(_createSamToolsSortCmd(iLauncher, inputFile, tmp_sorted_aligns_file_base))
127 cmd2Launch.append(_createSamToolsViewCmd(iLauncher, outputFile, tmp_sorted_aligns_file_name, options.header))
128 cmdStart = []
129 cmdFinish = []
130 lCmdsTuples.append(_map(iLauncher, cmd2Launch, cmdStart, cmdFinish))
131
132 iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, True)
133
134 if options.outputTar != None:
135 toTar(options.outputTar, samOutputNames)
136 #clean up temp files
137 for tmp_dir in tmp_dirs:
138 if os.path.exists( tmp_dir ):
139 shutil.rmtree( tmp_dir )
140 #print tmp_files
141 #for tmp in tmp_files:
142 # os.remove(tmp)
143
144
145 if __name__=="__main__": __main__()