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comparison commons/pyRepetUnit/fastaTranslation/allFrames/translateAfastaFileInAllFrameAndReplaceStopsByX_script.py @ 31:0ab839023fe4

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Uploaded
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 from commons.pyRepetUnit.fastaTranslation.allFrames.TranslateInAllFramesAndReplaceStopByX import TranslateInAllFramesAndReplaceStopByX
4 from commons.core.utils.FileUtils import FileUtils
5 import os
6 import sys
7 import getopt
8
9 #------------------------------------------------------------------------------
10
11 def help():
12
13 """
14 Give the command-line parameters.
15 """
16
17 print ""
18 print "usage: ",sys.argv[0],"[ options ]"
19 print "options:"
20 print " -h: this help"
21 print " -i: name of the nucleotidic input file (format='fasta')"
22 print " -o: name of the output file (default=inFileName+'_aa')"
23 print " -v: verbose (default=0/1/2)"
24 print " -c: clean"
25 print ""
26
27 #------------------------------------------------------------------------------
28
29 def main():
30
31 inFileName = ""
32 outFileName = ""
33 verbose = 0
34 clean = False
35
36 try:
37 opts = getopt.getopt(sys.argv[1:],"hi:o:v:c")[0]
38 except getopt.GetoptError, err:
39 print str(err)
40 help()
41 sys.exit(1)
42 for o,a in opts:
43 if o == "-h":
44 help()
45 sys.exit(0)
46 elif o == "-i":
47 inFileName = a
48 elif o == "-o":
49 outFileName = a
50 elif o == "-v":
51 verbose = int(a)
52 elif o == "-c":
53 clean = True
54
55 if inFileName == "":
56 print "*** Error: missing compulsory options"
57 help()
58 sys.exit(1)
59
60 if verbose > 0:
61 print "beginning of %s" % (sys.argv[0].split("/")[-1])
62 sys.stdout.flush()
63
64 if outFileName == "":
65 outFileName = "%s_aa" % ( inFileName )
66
67 iTIAFARSBX = TranslateInAllFramesAndReplaceStopByX()
68 iTIAFARSBX.setInputFile( inFileName )
69 iTIAFARSBX.setOutputFile( outFileName )
70 iTIAFARSBX.run( )
71
72 if clean == True:
73 os.remove( inFileName )
74
75 if verbose > 0:
76 if FileUtils.isRessourceExists( outFileName ) and not(FileUtils.isEmpty( outFileName )):
77 print "%s finished successfully" % (sys.argv[0].split("/")[-1])
78 sys.stdout.flush()
79 else:
80 print "warning %s execution failed" % (sys.argv[0].split("/")[-1])
81 sys.stdout.flush()
82
83 return 0
84
85 #------------------------------------------------------------------------------
86
87 if __name__ == '__main__':
88 main()