def Contract( self ): if self.mIsExpanded: self.mQueryAli, self.mSbjctAli = alignlib_lite.py_writeAlignataCompressed( self.mMapQuery2Sbjct ) self.mQueryFrom = self.mMapQuery2Sbjct.getRowFrom() self.mQueryTo = self.mMapQuery2Sbjct.getRowTo() self.mSbjctFrom = self.mMapQuery2Sbjct.getColFrom() self.mSbjctTo = self.mMapQuery2Sbjct.getColTo() self.mIsExpanded = False
def main(argv=None): if argv is None: argv = sys.argv parser = E.OptionParser( version= "%prog version: $Id: align_all_vs_all.py 2782 2009-09-10 11:40:29Z andreas $", usage=globals()["__doc__"]) parser.add_option("-s", "--sequences", dest="filename_sequences", type="string", help="input file with sequences") parser.set_defaults( filename_sequences=None, gop=-10.0, gep=-1.0, ) (options, args) = E.Start(parser, add_pipe_options=True) if options.filename_sequences: infile = open(options.filename_sequences, "r") else: infile = sys.stdin parser = FastaIterator.FastaIterator(infile) sequences = [] while 1: cur_record = iterator.next() if cur_record is None: break sequences.append( (cur_record.title, alignlib_lite.py_makeSequence(re.sub(" ", "", cur_record.sequence)))) if options.filename_sequences: infile.close() alignator = alignlib_lite.py_makeAlignatorFullDP(options.gop, options.gep) map_a2b = alignlib_lite.py_makeAlignataVector() nsequences = len(sequences) for x in range(0, nsequences - 1): for y in range(x + 1, nsequences): alignator.Align(sequences[x][1], sequences[y][1], map_a2b) row_ali, col_ali = alignlib_lite.py_writeAlignataCompressed( map_a2b) options.stdout.write( "%s\t%s\t%i\t%i\t%i\t%s\t%i\t%i\t%s\t%i\t%i\t%i\t%i\n" % (sequences[x][0], sequences[y][0], map_a2b.getScore(), map_a2b.getRowFrom(), map_a2b.getRowTo(), row_ali, map_a2b.getColFrom(), map_a2b.getColTo(), col_ali, map_a2b.getScore(), 100 * alignlib_lite.py_calculatePercentIdentity( map_a2b, sequences[x][1], sequences[y][1]), sequences[x][1].getLength(), sequences[y][1].getLength())) E.Stop()
def main( argv = None ): if argv == None: argv = sys.argv parser = E.OptionParser( version = "%prog version: $Id: align_all_vs_all.py 2782 2009-09-10 11:40:29Z andreas $", usage = globals()["__doc__"] ) parser.add_option("-s", "--sequences", dest="filename_sequences", type="string", help="input file with sequences" ) parser.set_defaults( filename_sequences = None, gop = -10.0, gep = -1.0, ) (options, args) = E.Start( parser, add_pipe_options = True ) if options.filename_sequences: infile = open(options.filename_sequences, "r") else: infile = sys.stdin parser = FastaIterator.FastaIterator( infile ) sequences = [] while 1: cur_record = iterator.next() if cur_record is None: break sequences.append( (cur_record.title, alignlib_lite.py_makeSequence(re.sub( " ", "", cur_record.sequence)) ) ) if options.filename_sequences: infile.close() alignator = alignlib_lite.py_makeAlignatorFullDP( options.gop, options.gep ) map_a2b = alignlib_lite.py_makeAlignataVector() nsequences = len(sequences) for x in range(0,nsequences-1): for y in range(x+1, nsequences): alignator.Align( sequences[x][1], sequences[y][1], map_a2b) row_ali, col_ali = alignlib_lite.py_writeAlignataCompressed( map_a2b ) options.stdout.write( "%s\t%s\t%i\t%i\t%i\t%s\t%i\t%i\t%s\t%i\t%i\t%i\t%i\n" % (\ sequences[x][0], sequences[y][0], map_a2b.getScore(), map_a2b.getRowFrom(), map_a2b.getRowTo(), row_ali, map_a2b.getColFrom(), map_a2b.getColTo(), col_ali, map_a2b.getScore(), 100 * alignlib_lite.py_calculatePercentIdentity( map_a2b, sequences[x][1], sequences[y][1]), sequences[x][1].getLength(), sequences[y][1].getLength() )) E.Stop()