Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/LaunchRefalign_old.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 import os
4 import sys
5 import getopt
6
7 import pyRepet.launcher.programLauncher
8 from commons.core.seq.BioseqDB import BioseqDB
9 from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
10
11
12 def help():
13 print
14 print "usage: launchRefalign.py [ options ]"
15 print "options:"
16 print " -h: this help"
17 print " -i: name of the input file (refseq is first, format='fasta')"
18 print " -r: keep the reference sequence"
19 print " -o: name of the output file (default=inFileName+'.fa_aln')"
20 print " -v: verbose (default=0)"
21 print
22
23
24 def main():
25 """
26 Launch 'refalign' to build a master-slave multiple sequence alignment.
27 """
28 inFileName = ""
29 keepRefseq = False
30 outFileName = ""
31 verbose = 0
32 try:
33 opts,args=getopt.getopt(sys.argv[1:],"hi:ro:v:")
34 except getopt.GetoptError, err:
35 print str(err); help(); sys.exit(1)
36 for o,a in opts:
37 if o == "-h":
38 help()
39 sys.exit(0)
40 elif o == "-i":
41 inFileName = a
42 elif o == "-r":
43 keepRefseq = True
44 elif o == "-o":
45 outFileName = a
46 elif o == "-v":
47 verbose = int(a)
48 if inFileName == "":
49 print "ERROR: missing compulsory options"
50 help()
51 sys.exit(1)
52
53 if verbose > 0:
54 print "START %s" % (sys.argv[0].split("/")[-1])
55 sys.stdout.flush()
56
57 if verbose > 0:
58 print "build a multiple alignment from '%s'..." % ( inFileName )
59 sys.stdout.flush()
60
61 if outFileName == "":
62 outFileName = "%s.fa_aln" % ( inFileName )
63
64 csh = ChangeSequenceHeaders()
65 csh.setInputFile( inFileName )
66 csh.setFormat( "fasta" )
67 csh.setStep( 1 )
68 csh.setPrefix( "seq" )
69 csh.setLinkFile( inFileName+".shortHlink" )
70 csh.setOutputFile( inFileName+".shortH" )
71 csh.setVerbosityLevel( verbose - 1 )
72 csh.run()
73
74 bsDB = BioseqDB( inFileName+".shortH" )
75 bsDB.upCase()
76 bsDB.save( inFileName+".shortHtmp" )
77 del bsDB
78 os.rename( inFileName+".shortHtmp", inFileName+".shortH" )
79
80 pL = pyRepet.launcher.programLauncher.programLauncher( inFileName+".shortH" )
81 if keepRefseq:
82 pL.launchRefalign( outFileName=inFileName+".shortH.fa_aln", refseqName="seq1", verbose=verbose )
83 else:
84 pL.launchRefalign( outFileName=inFileName+".shortH.fa_aln", verbose=verbose )
85
86 csh.setInputFile( inFileName+".shortH.fa_aln" )
87 csh.setFormat( "fasta" )
88 csh.setStep( 2 )
89 csh.setLinkFile( inFileName+".shortHlink" )
90 csh.setOutputFile( outFileName )
91 csh.setVerbosityLevel( verbose - 1 )
92 csh.run()
93
94 for f in [ inFileName+".shortH", inFileName+".shortHlink", inFileName+".shortH.fa_aln" ]:
95 os.remove( f )
96
97 if verbose > 0:
98 print "END %s" % (sys.argv[0].split("/")[-1])
99 sys.stdout.flush()
100
101 return 0
102
103
104 if __name__ == "__main__":
105 main()