Mercurial > repos > yufei-luo > s_mart

comparison commons/tools/blast2align.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 sys
4 import getopt
5
6
7 def help():
8 print
9 print "usage: blast2align.py [ options ]"
10 print "options:"
11 print " -h: this help"
12 print " -i: input file name (format=tabulated BLAST)"
13 print " -o: output file name (format=align, default=inFileName+'.align')"
14 print
15
16
17 def blast2align( inFile, outFile ):
18 inFileHandler = open( inFile, "r" )
19 outFileHandler = open( outFile, "w" )
20 while True:
21 line = inFileHandler.readline()
22 if line == "":
23 break
24 if line[0] != "#":
25 data = line.split("\t")
26 qryName = data[0]
27 sbjName = data[1]
28 percId = data[2]
29 qryStart = data[6]
30 qryEnd = data[7]
31 sbjStart = data[8]
32 sbjEnd = data[9]
33 Eval = data[10]
34 bitScore = data[11][:-1]
35 string = "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( qryName, qryStart, qryEnd, sbjName, sbjStart, sbjEnd, Eval, bitScore, percId )
36 outFileHandler.write( string )
37 inFileHandler.close()
38 outFileHandler.close()
39
40
41 def main():
42 inFileName = ""
43 outFileName = ""
44
45 try:
46 opts, args = getopt.getopt(sys.argv[1:],"hi:o:")
47 except getopt.GetoptError, err:
48 sys.stderr.write( "%s\n" % str(err) )
49 help()
50 sys.exit(1)
51 for o,a in opts:
52 if o == "-h":
53 help()
54 sys.exit(0)
55 elif o == "-i":
56 inFileName = a
57 elif o == "-o":
58 outFileName = a
59
60 if inFileName == "":
61 msg = "ERROR: missing input file name (-i)"
62 sys.stderr.write( "%s\n" % msg )
63 help()
64 sys.exit(1)
65
66 if outFileName == "":
67 outFileName = inFileName + ".align"
68
69 blast2align( inFileName, outFileName )
70
71 return 0
72
73
74 if __name__ == "__main__":
75 main()