Mercurial > repos > yufei-luo > s_mart

comparison commons/pyRepetUnit/profilesDB/tests/completeProfilesDBFromAFileWithProfilesList_script.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 #!/usr/bin/env python
2 '''
3 Created on 19 mai 2009
4
5 @author: choede
6 '''
7
8 import commons.pyRepetUnit.profilesDB.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber
9 import user, os, sys, getopt, exceptions
10 from pyRepet.util.file.FileUtils import *
11
12 #------------------------------------------------------------------------------
13
14 def help():
15
16 """
17 Give the command-line parameters.
18 """
19
20 print ""
21 print "usage: ",sys.argv[0],"[ options ]"
22 print "options:"
23 print " -h: this help"
24 print " -d: name of profiles databank (format='pfam')"
25 print " -l: name of the profiles list file (name or accession number, default=profiles name)"
26 print " -o: name of the output file (default=profiles list file+'.getz')"
27 print " -v: verbose (default=0/1/2)"
28 print " -n: pfam accession number (default=Not set)"
29 print ""
30
31 #------------------------------------------------------------------------------
32
33 def main():
34
35 DBFileName = ""
36 outFileName = ""
37 verbose = 0
38 listFileName = ""
39 accNumber = False
40
41 try:
42 opts,args=getopt.getopt(sys.argv[1:],"hd:l:o:v:n")
43 except getopt.GetoptError, err:
44 print str(err)
45 help()
46 sys.exit(1)
47 for o,a in opts:
48 if o == "-h":
49 help()
50 sys.exit(0)
51 elif o == "-d":
52 DBFileName = a
53 elif o == "-l":
54 listFileName = a
55 elif o == "-o":
56 outFileName = a
57 elif o == "-v":
58 verbose = int(a)
59 elif o == "-n":
60 accNumber = True
61
62
63 if DBFileName == "" or listFileName == "":
64 print "*** Error: missing compulsory options"
65 help()
66 sys.exit(1)
67
68 if verbose > 0:
69 print "beginning of %s" % (sys.argv[0].split("/")[-1])
70 sys.stdout.flush()
71
72 if outFileName == "":
73 outFileName = "%s.getz" % ( listFileName )
74
75 CompleteProfilesDB = commons.pyRepetUnit.profilesDB.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber()
76 CompleteProfilesDB.setProfilesDBFile ( DBFileName )
77 CompleteProfilesDB.setProfilesToAdd ( listFileName )
78 if accNumber == True:
79 CompleteProfilesDB.setPfamAccNumberKeys ()
80 if verbose > 0:
81 print "The profiles list is in Accession number"
82 sys.stdout.flush()
83 getzCmd = CompleteProfilesDB.CmdToCompleteProfileDB()
84 f = open( outFileName , 'w')
85 f.write ( getzCmd )
86 f.close()
87
88 if verbose > 0:
89 fileUtils = FileUtils( )
90 if fileUtils.isRessourceExists( outFileName ) and not(fileUtils.isFileEmpty( outFileName )):
91 print "%s finished successfully" % (sys.argv[0].split("/")[-1])
92 sys.stdout.flush()
93 else:
94 print "warning %s execution failed" % (sys.argv[0].split("/")[-1])
95 sys.stdout.flush()
96
97 return 0
98
99 #------------------------------------------------------------------------------
100
101 if __name__ == '__main__':
102 main()