annotate SMART/DiffExpAnal/compareOverlapping_parallel.py @ 18:94ab73e8a190

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1 #! /usr/bin/env python
2 #This program is a wrapp for CompareOverlapping.py.
3 import optparse, os, sys, subprocess, tempfile, shutil, tarfile, glob
4 import os, struct, time, random
5 from optparse import OptionParser
6 from commons.core.parsing.ParserChooser import ParserChooser
7 from commons.core.writer.Gff3Writer import Gff3Writer
8 from SMART.Java.Python.CompareOverlapping import CompareOverlapping
9 from SMART.Java.Python.structure.Transcript import Transcript
10 from SMART.Java.Python.structure.Interval import Interval
11 from SMART.Java.Python.ncList.NCList import NCList
12 from SMART.Java.Python.ncList.NCListCursor import NCListCursor
13 from SMART.Java.Python.ncList.NCListFilePickle import NCListFilePickle, NCListFileUnpickle
14 from SMART.Java.Python.ncList.FileSorter import FileSorter
15 from SMART.Java.Python.misc.Progress import Progress
16 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
17 from SMART.Java.Python.misc import Utils
18 
19 
20 
21 def stop_err( msg ):
22 	sys.stderr.write( "%s\n" % msg )
23 	sys.exit()
24 
25 def toTar(tarFileName, overlapOutputNames):
26 	dir = os.path.dirname(tarFileName)	
27 	tfile = tarfile.open(tarFileName + ".tmp.tar", "w")
28 	currentPath = os.getcwd()
29 	os.chdir(dir)
30 	for file in overlapOutputNames:
31 		relativeFileName = os.path.basename(file)
32 		tfile.add(relativeFileName)
33 	os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName))
34 	tfile.close()
35 	os.chdir(currentPath)
36 
37 def __main__():
38 	description = "Compare Overlapping wrapp script: Get the a list of data which overlap with a reference set. [Category: Data Comparison]"
39 	parser = OptionParser(description = description)
40 	parser.add_option("-i", "--input1",		   dest="inputFileName1", action="store",					 type="string", help="input file 1 (for annotation) [compulsory] [format: file in transcript format given by -f]")
41 	parser.add_option("-f", "--format1",		  dest="format1",		action="store",					 type="string", help="format of file 1 [compulsory] [format: transcript file format]")
42 	parser.add_option("", "--inputTxt", 		dest="inputTxt", 		action="store", 				type="string", 	help="input, a txt file for a list of input reads files. Should identify all reads files format, given by -g [compulsory]")
43 	#parser.add_option("-j", "--input2",		   dest="inputFileName2", action="store",	default="inputRead",	 type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")
44 	parser.add_option("-g", "--format2",		  dest="format2",		action="store",				 type="string", help="format of file 2 [compulsory] [format: transcript file format]")
45 	#parser.add_option("-o", "--output",		   dest="output",		 action="store",	  default=None,  type="string", help="output file [compulsory] [format: output file in GFF3 format]")
46 	parser.add_option("-S", "--start1",		   dest="start1",		 action="store",	  default=None,  type="int",	help="only consider the n first nucleotides of the transcripts in file 1 (do not use it with -U) [format: int]")
47 	parser.add_option("-s", "--start2",		   dest="start2",		 action="store",	  default=None,  type="int",	help="only consider the n first nucleotides of the transcripts in file 2 (do not use it with -u) [format: int]")
48 	parser.add_option("-U", "--end1",			 dest="end1",		   action="store",	  default=None,  type="int",	help="only consider the n last nucleotides of the transcripts in file 1 (do not use it with -S) [format: int]")
49 	parser.add_option("-u", "--end2",			 dest="end2",		   action="store",	  default=None,  type="int",	help="only consider the n last nucleotides of the transcripts in file 2 (do not use it with -s) [format: int]")
50 	parser.add_option("-t", "--intron",		   dest="introns",		action="store_true", default=False,				help="also report introns [format: bool] [default: false]")
51 	parser.add_option("-E", "--5primeExtension1", dest="fivePrime1",	 action="store",	  default=None,  type="int",	help="extension towards 5' in file 1 [format: int]")
52 	parser.add_option("-e", "--5primeExtension2", dest="fivePrime2",	 action="store",	  default=None,  type="int",	help="extension towards 5' in file 2 [format: int]")
53 	parser.add_option("-N", "--3primeExtension1", dest="threePrime1",	action="store",	  default=None,  type="int",	help="extension towards 3' in file 1 [format: int]")
54 	parser.add_option("-n", "--3primeExtension2", dest="threePrime2",	action="store",	  default=None,  type="int",	help="extension towards 3' in file 2 [format: int]")
55 	parser.add_option("-c", "--colinear",		 dest="colinear",	   action="store_true", default=False,				help="colinear only [format: bool] [default: false]")
56 	parser.add_option("-a", "--antisense",		dest="antisense",	  action="store_true", default=False,				help="antisense only [format: bool] [default: false]")
57 	parser.add_option("-d", "--distance",		 dest="distance",	   action="store",	  default=None,	 type="int",	help="accept some distance between query and reference [format: int]")
58 	parser.add_option("-k", "--included",		 dest="included",	   action="store_true", default=False,				help="keep only elements from file 1 which are included in an element of file 2 [format: bool] [default: false]")
59 	parser.add_option("-K", "--including",		dest="including",	  action="store_true", default=False,				help="keep only elements from file 2 which are included in an element of file 1 [format: bool] [default: false]")
60 	parser.add_option("-m", "--minOverlap",	   dest="minOverlap",	 action="store",	  default=None,	 type="int",	help="minimum number of nucleotides overlapping to declare an overlap [format: int] [default: 1]")
61 	parser.add_option("-p", "--pcOverlap",		dest="pcOverlap",	  action="store",	  default=None,  type="int",	help="minimum percentage of nucleotides to overlap to declare an overlap [format: int]")
62 	parser.add_option("-O", "--notOverlapping",   dest="notOverlapping", action="store_true", default=False,				help="also output not overlapping data [format: bool] [default: false]")
63 	parser.add_option("-x", "--exclude",		  dest="exclude",		action="store_true", default=False,				help="invert the match [format: bool] [default: false]")
64 	parser.add_option("-v", "--verbosity",		dest="verbosity",	  action="store",	  default=1,	 type="int",	help="trace level [format: int]")
65 	parser.add_option('', '--tar', dest='outputTar', default=None, help='output all SAM results in a tar file.' )
66 	parser.add_option( '', '--outTxt', dest='outTxtFile', help='The output list of results files on txt format.[compulsory]' )
67 	(options, args) = parser.parse_args()
68 	
69 	
70 	#Parse the input txt file and read a list of BAM files.
71 	file = open(options.inputTxt, "r")
72 	lines = file.readlines()
73 	inputFileNames = []
74 	overlapOutputNames = []
75 	outputName = options.outTxtFile
76 	resDirName = os.path.dirname(outputName) + "/"
77 	#Write output txt file and define all output sam file names.
78 	out = open(outputName, "w")
79 	for line in lines:
80 		tab = line.split()
81 		inputFileNames.append(tab[1])
82 		overlapOutName = resDirName + tab[0] + '_overlapOut_%s.gff3' % random.randrange(0, 10000)
83 		overlapOutputNames.append(overlapOutName)
84 		out.write(tab[0] + '\t' + overlapOutName  + '\n')
85 	file.close()
86 	out.close()
87 	
88 	#construction the commandes for each input file
89 	cmds = []
90 	for i in range(len(inputFileNames)):
91 		absFile = sys.argv[0]
92 		absDir = os.path.dirname(absFile)
93 		parentDir = os.path.abspath(os.path.join(absDir, os.path.pardir))
94 		cmd = "python %s/Java/Python/CompareOverlappingSmallQuery.py " % parentDir
95 		opts = "-i %s -f %s -j %s -g %s -o %s " % (options.inputFileName1, options.format1, inputFileNames[i], options.format2, overlapOutputNames[i])
96 		#if options.start1 != None:
97 		#	opts += "-S %s " % options.start1
98 		#if options.start2 != None:
99 		#	opts += "-s %s " % options.start2
00 		#if options.end1 != None:
01 		#	opts += "-U %s " % options.end1
02 		#if options.end2 != None:
03 		#	opts += "-u %s " % options.end2
04 		#if options.fivePrime1 != None:
05 		#	opts += "-E %s " % options.fivePrime1
06 		#if options.fivePrime2 != None:
07 		#	opts += "-e %s " % options.fivePrime2
08 		#if options.threePrime1 != None:
09 		#	opts += "-N %s " % options.threePrime1
10 		#if options.threePrime2 != None:
11 		#	opts += "-n %s " % options.threePrime2
12 		#if options.colinear:
13 		#	opts += "-c "
14 		#if options.antisense:
15 		#	opts +="-a "
16 		#if options.included:
17 		#	opts += "-k "
18 		#if options.including:
19 		#	opts += "-K "
20 		#if options.pcOverlap != None:
21 		#	opts += "-p %s " % options.pcOverlap
22 		if options.notOverlapping:
23 			opts += "-O "
24 		if options.exclude:
25 			opts += "-x "
26 		if options.distance != None:
27 			opts += "-d %s " % options.distance
28 		#if options.minOverlap != None:
29 		#	opts += "-m %s " % options.minOverlap
30 		cmd += opts
31 		cmds.append(cmd)
32 
33 
34 	print "les commandes sont %s \n" % cmds
35 
36 	tmp_files = []	
37 	for i in range(len(cmds)):
38 		try:
39 			tmp_out = tempfile.NamedTemporaryFile().name
40 			tmp_files.append(tmp_out)
41 			tmp_stdout = open( tmp_out, 'wb' )
42 			tmp_err = tempfile.NamedTemporaryFile().name
43 			tmp_files.append(tmp_err)
44 			tmp_stderr = open( tmp_err, 'wb' )
45 			proc = subprocess.Popen( args=cmds[i], shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr )
46 			returncode = proc.wait()
47 			tmp_stderr.close()
48 			# get stderr, allowing for case where it's very large
49 			tmp_stderr = open( tmp_err, 'rb' )
50 			stderr = ''
51 			buffsize = 1048576
52 			try:
53 				while True:
54 					stderr += tmp_stderr.read( buffsize )
55 					if not stderr or len( stderr ) % buffsize != 0:
56 						break
57 			except OverflowError:
58 				pass
59 			tmp_stdout.close()
60 			tmp_stderr.close()
61 			if returncode != 0:
62 				raise Exception, stderr
63 		except Exception, e:
64 			stop_err( 'Error in :\n' + str( e ) )
65 
66 	if options.outputTar != None:
67 		toTar(options.outputTar, overlapOutputNames)	
68 	
69 	for tmp_file in tmp_files:
70 		os.remove(tmp_file)
71 
72 
73 if __name__=="__main__": __main__()		
74 		
75