alignator = alignlib_lite.py_makeAlignatorDPFull(alignlib_lite.py_ALIGNMENT_LOCAL, param_gop, param_gep) map_query2token = alignlib_lite.py_makeAlignmentVector() for line in sys.stdin: if line[0] == "#": continue query_token, sbjct_token, query_sequence, sbjct_sequence = string.split(line[:-1], "\t") map_query2token.clear() row = alignlib_lite.py_makeSequence(query_sequence) col = alignlib_lite.py_makeSequence(sbjct_sequence) alignator.align(map_query2token, row, col) pidentity = 100.0 * alignlib_lite.py_calculatePercentIdentity(map_query2token, row, col) psimilarity = 100.0 * alignlib_lite.py_calculatePercentSimilarity(map_query2token) print string.join( map( str, ( query_token, sbjct_token, map_query2token.getScore(), alignlib_lite.py_AlignmentFormatEmissions(map_query2token), pidentity, psimilarity, map_query2token.getNumGaps(), ), ), "\t",
alignator = alignlib_lite.py_makeAlignatorDPFull( alignlib_lite.py_ALIGNMENT_LOCAL, param_gop, param_gep) map_query2token = alignlib_lite.py_makeAlignmentVector() for line in sys.stdin: if line[0] == "#": continue query_token, sbjct_token, query_sequence, sbjct_sequence = string.split( line[:-1], "\t") map_query2token.clear() row = alignlib_lite.py_makeSequence(query_sequence) col = alignlib_lite.py_makeSequence(sbjct_sequence) alignator.align(map_query2token, row, col) pidentity = 100.0 * \ alignlib_lite.py_calculatePercentIdentity( map_query2token, row, col) psimilarity = 100.0 * \ alignlib_lite.py_calculatePercentSimilarity(map_query2token) print string.join( map(str, (query_token, sbjct_token, map_query2token.getScore(), alignlib_lite.py_AlignmentFormatEmissions(map_query2token), pidentity, psimilarity, map_query2token.getNumGaps())), "\t") if __name__ == "__main__": sys.exit(main(sys.argv))
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()