Mercurial > repos > urgi-team > teiso

comparison TEiso/ClosestToStartSite_Wrapper.py @ 1:15d6811e6bf5 draft

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author urgi-team
date Tue, 24 May 2016 08:59:28 -0400
parents 3d22562b4489
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0:3d22562b4489 1:15d6811e6bf5
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 2
3 3
4 import subprocess, tempfile, sys, os, glob, shutil, time 4 import subprocess, tempfile, sys, os, glob, shutil, time
5 from optparse import OptionParser 5 from optparse import OptionParser
6 from commons.core.utils.RepetOptionParser import RepetOptionParser
7 6
8 7
9 class ClosestToStartSiteWrapper(object): 8 class ClosestToStartSiteWrapper(object):
10 9
11 def __init__(self): 10 def __init__(self):
16 sys.stderr.write( "%s\n" % msg ) 15 sys.stderr.write( "%s\n" % msg )
17 sys.exit() 16 sys.exit()
18 17
19 18
20 def setAttributesFromCmdLine(self): 19 def setAttributesFromCmdLine(self):
21 self._toolVersion = "1.0" 20 description = "ClosestToStartSite"
22 description = "ClosestToStartSite version %s" % self._toolVersion 21 epilog = "\nParser a bed file and create a bed file to create a report about positions of features A to features B. \n"
23 epilog = "\n parses a bed file and create a bed file to create a report about positions of features A to features B. \n" 22 epilog +="it can also add the class code of features A. \n"
24 epilog += "example: ClosestToStartSite.py -i <inputFile> -o <outputFile>\n" 23 epilog += "example: ClosestToStartSite.py -i <inputFile> -c <cuff_in.tmap> -o <outputFile>\n"
25 parser = RepetOptionParser(description = description, epilog = epilog, version = self._toolVersion) 24 parser = OptionParser(description = description, version = "1.0")
26 parser.add_option("-i", "--inputFile", dest = "inputFile", action = "store", type = "string", help = "Input GTF File name(transcript.gtf of Cufflinks).", default = "") 25 parser.add_option("-i", "--inputFile", dest = "inputFile", action = "store", type = "string", help = "input bed file", default = "")
26 parser.add_option("-c", "--cuffcom_tmap", dest = "cuffcom_tmap", action = "store", type = "string", help = "input gtf file", default = "")
27 parser.add_option("-o", "--outputFile", dest = "outputFile", action = "store", type = "string", help = "output Bed File name", default = "") 27 parser.add_option("-o", "--outputFile", dest = "outputFile", action = "store", type = "string", help = "output Bed File name", default = "")
28 parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "Verbosity [optional] [default: 3]",default = 3) 28 #parser.add_option("-t", "--outputFileclasscode", dest = "outputFile_classcode", action = "store", type = "string", help = "output Bed File name with class code.", default = "")
29 parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 3]",default = 3)
29 options = parser.parse_args()[0] 30 options = parser.parse_args()[0]
30 self._setAttributesFromOptions(options) 31 self._setAttributesFromOptions(options)
31 32
32 def _setAttributesFromOptions(self, options): 33 def _setAttributesFromOptions(self, options):
33 self._options = options 34 self._options = options
34 35
35 def run(self): 36 def run(self):
36 prg = "ClosestToStartSite.py" 37 prg = "ClosestToStartSite.py"
37 args = "" 38 args = ""
38 args += "-i %s" % self._options.inputFile 39 args += "-i %s" % self._options.inputFile
40 args += " "
41 args += "-o %s" % self._options.outputFile
42 if self._options.cuffcom_tmap != "":
43 args += " "
44 args += "-c %s" % self._options.cuffcom_tmap
39 cmd = "%s %s" %(prg, args) 45 cmd = "%s %s" %(prg, args)
40 print cmd 46 print cmd
41 47
42 try: 48 try:
43 tmp_err = tempfile.NamedTemporaryFile().name 49 tmp_err = tempfile.NamedTemporaryFile().name