Mercurial > repos > urgi-team > teiso
view TEisotools-1.1.a/commons/core/coord/align2set.py @ 15:255c852351c5 draft
Uploaded
author | urgi-team |
---|---|
date | Thu, 21 Jul 2016 07:36:44 -0400 |
parents | feef9a0db09d |
children |
line wrap: on
line source
#!/usr/bin/env python import sys import getopt from commons.core.coord.Align import Align def help(): print print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] ) print "options:" print " -h: this help" print " -i: input file name (format='align')" print " -o: output file name (format='set', default=inFileName+'.set')" print " -v: verbosity level (default=0/1)" print def align2set( inFileName, outFileName ): alignFileHandler = open( inFileName, "r" ) setFileHandler = open( outFileName, "w" ) iAlign = Align() countAlign = 0 while True: line = alignFileHandler.readline() if line == "": break countAlign += 1 iAlign.setFromString( line, "\t" ) setFileHandler.write( "%i\t%s\t%s\t%i\t%i\n" % ( countAlign, iAlign.getSubjectName(), iAlign.getQueryName(), iAlign.getQueryStart(), iAlign.getQueryEnd() ) ) alignFileHandler.close() setFileHandler.close() def main(): inFileName = "" outFileName = "" verbose = 0 try: opts, args = getopt.getopt( sys.argv[1:], "hi:o:v:" ) except getopt.GetoptError, err: print str(err) help() sys.exit(1) for o,a in opts: if o == "-h": help() sys.exit(0) elif o == "-i": inFileName = a elif o == "-o": outFileName = a elif o == "-v": verbose = int(a) if inFileName == "": print "ERROR: missing input file name" help() sys.exit(1) if verbose > 0: print "START %s" % ( sys.argv[0].split("/")[-1] ) sys.stdout.flush() if outFileName == "": outFileName = "%s.set" % ( inFileName ) #TODO: move 'align2set' into 'AlignUtils.convertAlignFileIntoPSetFile' with a test # AlignUtils.convertAlignFileIntoPSetFile( inFileName, outFileName ) align2set( inFileName, outFileName ) if verbose > 0: print "END %s" % ( sys.argv[0].split("/")[-1] ) sys.stdout.flush() return 0 if __name__ == "__main__": main()