Mercurial > repos > urgi-team > teiso
comparison TEisotools-1.1.a/commons/core/coord/align2set.py @ 16:836ce3d9d47a draft default tip
Uploaded
| author | urgi-team |
|---|---|
| date | Thu, 21 Jul 2016 07:42:47 -0400 |
| parents | 255c852351c5 |
| children |
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| 15:255c852351c5 | 16:836ce3d9d47a |
|---|---|
| 1 #!/usr/bin/env python | |
| 2 | |
| 3 import sys | |
| 4 import getopt | |
| 5 from commons.core.coord.Align import Align | |
| 6 | |
| 7 def help(): | |
| 8 print | |
| 9 print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] ) | |
| 10 print "options:" | |
| 11 print " -h: this help" | |
| 12 print " -i: input file name (format='align')" | |
| 13 print " -o: output file name (format='set', default=inFileName+'.set')" | |
| 14 print " -v: verbosity level (default=0/1)" | |
| 15 print | |
| 16 | |
| 17 | |
| 18 def align2set( inFileName, outFileName ): | |
| 19 alignFileHandler = open( inFileName, "r" ) | |
| 20 setFileHandler = open( outFileName, "w" ) | |
| 21 iAlign = Align() | |
| 22 countAlign = 0 | |
| 23 while True: | |
| 24 line = alignFileHandler.readline() | |
| 25 if line == "": | |
| 26 break | |
| 27 countAlign += 1 | |
| 28 iAlign.setFromString( line, "\t" ) | |
| 29 setFileHandler.write( "%i\t%s\t%s\t%i\t%i\n" % ( countAlign, | |
| 30 iAlign.getSubjectName(), | |
| 31 iAlign.getQueryName(), | |
| 32 iAlign.getQueryStart(), | |
| 33 iAlign.getQueryEnd() ) ) | |
| 34 alignFileHandler.close() | |
| 35 setFileHandler.close() | |
| 36 | |
| 37 | |
| 38 def main(): | |
| 39 | |
| 40 inFileName = "" | |
| 41 outFileName = "" | |
| 42 verbose = 0 | |
| 43 | |
| 44 try: | |
| 45 opts, args = getopt.getopt( sys.argv[1:], "hi:o:v:" ) | |
| 46 except getopt.GetoptError, err: | |
| 47 print str(err) | |
| 48 help() | |
| 49 sys.exit(1) | |
| 50 for o,a in opts: | |
| 51 if o == "-h": | |
| 52 help() | |
| 53 sys.exit(0) | |
| 54 elif o == "-i": | |
| 55 inFileName = a | |
| 56 elif o == "-o": | |
| 57 outFileName = a | |
| 58 elif o == "-v": | |
| 59 verbose = int(a) | |
| 60 | |
| 61 if inFileName == "": | |
| 62 print "ERROR: missing input file name" | |
| 63 help() | |
| 64 sys.exit(1) | |
| 65 | |
| 66 if verbose > 0: | |
| 67 print "START %s" % ( sys.argv[0].split("/")[-1] ) | |
| 68 sys.stdout.flush() | |
| 69 | |
| 70 if outFileName == "": | |
| 71 outFileName = "%s.set" % ( inFileName ) | |
| 72 | |
| 73 #TODO: move 'align2set' into 'AlignUtils.convertAlignFileIntoPSetFile' with a test | |
| 74 # AlignUtils.convertAlignFileIntoPSetFile( inFileName, outFileName ) | |
| 75 | |
| 76 align2set( inFileName, outFileName ) | |
| 77 | |
| 78 if verbose > 0: | |
| 79 print "END %s" % ( sys.argv[0].split("/")[-1] ) | |
| 80 sys.stdout.flush() | |
| 81 | |
| 82 return 0 | |
| 83 | |
| 84 | |
| 85 if __name__ == "__main__": | |
| 86 main() |