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

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1 #!/usr/bin/env python
2 
3 
4 import subprocess, tempfile, sys, os, glob, shutil, time
5 from optparse import OptionParser
6 
7 
8 class ClosestToStartSiteWrapper(object):
9 
10     def __init__(self):
11         self._options = None
12         
13         
14     def stop_err(self, msg ):
15         sys.stderr.write( "%s\n" % msg )
16         sys.exit()
17         
18         
19     def setAttributesFromCmdLine(self):
20         description = "ClosestToStartSite"
21         epilog = "\nParser 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"
23         epilog += "example: ClosestToStartSite.py -i <inputFile> -c <cuff_in.tmap> -o <outputFile>\n"
24         parser = OptionParser(description = description, version = "1.0")
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 = "")
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)
30         options = parser.parse_args()[0]
31         self._setAttributesFromOptions(options)
32 
33     def _setAttributesFromOptions(self, options):
34         self._options = options
35 
36     def run(self):
37         prg = "ClosestToStartSite.py"
38         args = ""
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
45         cmd = "%s %s" %(prg, args)
46         print cmd
47         
48         try:
49             tmp_err = tempfile.NamedTemporaryFile().name
50             tmp_stderr = open( tmp_err, 'wb' )
51             proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stderr=tmp_stderr )
52             returncode = proc.wait()
53             tmp_stderr.close()
54             # get stderr, allowing for case where it's very large
55             tmp_stderr = open( tmp_err, 'rb' )
56             stderr = ''
57             buffsize = 1048576
58             try:
59                 while True:
60                     stderr += tmp_stderr.read( buffsize )
61                     if not stderr or len( stderr ) % buffsize != 0:
62                         break
63             except OverflowError:
64                 pass
65             tmp_stderr.close()
66             if stderr:
67                 raise Exception, stderr
68         except Exception, e:
69             self.stop_err( 'Error in ClosestToStartSite:\n' + str( e ) ) 
70         
71 if __name__ == "__main__":
72     iWrapper = ClosestToStartSiteWrapper()
73     iWrapper.setAttributesFromCmdLine()
74     iWrapper.run()