def convertMali2Mali(mali): """convert a mali to a profile.""" new_mali = alignlib_lite.py_makeMultipleAlignment() for id in mali.getIdentifiers(): s = alignlib_lite.py_makeAlignatumFromString(mali[id]) s.thisown = 0 new_mali.addAlignatum(s) return new_mali
def readPicasso(infile): """read alignment in the non-defined picasso format. """ mali = alignlib_lite.py_makeMultipleAlignment() while 1: line = infile.readline() if not line: break x = re.search("\d+\s+([A-Z\-\.]*)\s+\d+", line) if x: s = x.groups()[0] a = alignlib_lite.py_makeAlignatumFromString(s) a.thisown = 0 mali.addAlignatum(a) return mali
def readPicasso( infile ): """read alignment in the non-defined picasso format. """ mali = alignlib_lite.py_makeMultipleAlignment() while 1: line = infile.readline() if not line: break x = re.search( "\d+\s+([A-Z\-\.]*)\s+\d+", line) if x: s = x.groups()[0] a = alignlib_lite.py_makeAlignatumFromString(s) a.thisown = 0 mali.addAlignatum( a ) return mali
def main(argv=None): """script main. parses command line options in sys.argv, unless *argv* is given. """ if argv is None: argv = sys.argv parser = E.OptionParser( version="%prog version: $Id: sequences2mali.py 2782 2009-09-10 11:40:29Z andreas $", usage=globals()["__doc__"]) parser.add_option("-i", "--input-format", dest="input_format", type="choice", choices=( "plain", "fasta", "clustal", "stockholm", "phylip"), help="input format of multiple alignment") parser.add_option("-o", "--output-format", dest="output_format", type="choice", choices=("plain", "fasta", "stockholm", "phylip"), help="output format of multiple alignment") parser.add_option("-m", "--method", dest="method", type="choice", choices=("add",), help="""method to use to build multiple alignment.""") parser.add_option("-p", "--parameters", dest="parameters", type="string", help="parameter stack for methods that require one.") parser.add_option("-a", "--alignment-method", dest="alignment_method", type="choice", choices=("sw", "nw"), help="alignment_method [%default].") parser.set_defaults( input_format="fasta", output_format="fasta", method=None, parameters="", gop=-10.0, gep=-1.0, alignment_method="sw", ) (options, args) = E.Start(parser) options.parameters = options.parameters.split(",") iterator = FastaIterator.iterate(sys.stdin) if options.method == "add": mali = Mali.Mali() mali.readFromFile( open(options.parameters[0], "r"), format=options.input_format) del options.parameters[0] old_length = mali.getLength() new_mali = convertMali2Mali(mali) if options.alignment_method == "sw": alignator = alignlib_lite.py_makeAlignatorFullDP( options.gop, options.gep) else: alignator = alignlib_lite.py_makeAlignatorFullDPGlobal( options.gop, options.gep) while 1: cur_record = iterator.next() if cur_record is None: break map_mali2seq = alignlib_lite.py_makeAlignataVector() sequence = alignlib_lite.py_makeSequence(cur_record.sequence) profile = alignlib_lite.py_makeProfileFromMali(new_mali) if options.loglevel >= 4: options.stdlog.write(profile.Write()) alignator.Align(profile, sequence, map_mali2seq) if options.loglevel >= 3: options.stdlog.write(map_mali2seq.Write()) # add sequence to mali a = alignlib_lite.py_makeAlignatumFromString(cur_record.sequence) a.thisown = 0 new_mali.addAlignatum(a, map_mali2seq, 1, 1, 1, 1, 1) id = cur_record.title mali.mIdentifiers.append(id) mali.mMali[id] = Mali.AlignedString(id, 0, len( cur_record.sequence), new_mali.getRow(new_mali.getWidth() - 1).getString()) # substitute for x in range(old_length): mali.mMali[mali.mIdentifiers[x]].mString = new_mali.getRow( x).getString() mali.writeToFile(sys.stdout, format=options.output_format) E.Stop()
def main(argv=None): """script main. parses command line options in sys.argv, unless *argv* is given. """ if argv == None: argv = sys.argv parser = E.OptionParser( version= "%prog version: $Id: sequences2mali.py 2782 2009-09-10 11:40:29Z andreas $", usage=globals()["__doc__"]) parser.add_option("-i", "--input-format", dest="input_format", type="choice", choices=("plain", "fasta", "clustal", "stockholm", "phylip"), help="input format of multiple alignment") parser.add_option("-o", "--output-format", dest="output_format", type="choice", choices=("plain", "fasta", "stockholm", "phylip"), help="output format of multiple alignment") parser.add_option("-m", "--method", dest="method", type="choice", choices=("add", ), help="""method to use to build multiple alignment.""") parser.add_option("-p", "--parameters", dest="parameters", type="string", help="parameter stack for methods that require one.") parser.add_option("-a", "--alignment-method", dest="alignment_method", type="choice", choices=("sw", "nw"), help="alignment_method [%default].") parser.set_defaults( input_format="fasta", output_format="fasta", method=None, parameters="", gop=-10.0, gep=-1.0, alignment_method="sw", ) (options, args) = E.Start(parser) options.parameters = options.parameters.split(",") iterator = FastaIterator.iterate(sys.stdin) if options.method == "add": mali = Mali.Mali() mali.readFromFile(open(options.parameters[0], "r"), format=options.input_format) del options.parameters[0] old_length = mali.getLength() new_mali = convertMali2Mali(mali) if options.alignment_method == "sw": alignator = alignlib_lite.py_makeAlignatorFullDP( options.gop, options.gep) else: alignator = alignlib_lite.py_makeAlignatorFullDPGlobal( options.gop, options.gep) while 1: cur_record = iterator.next() if cur_record is None: break map_mali2seq = alignlib_lite.py_makeAlignataVector() sequence = alignlib_lite.py_makeSequence(cur_record.sequence) profile = alignlib_lite.py_makeProfileFromMali(new_mali) if options.loglevel >= 4: options.stdlog.write(profile.Write()) alignator.Align(profile, sequence, map_mali2seq) if options.loglevel >= 3: options.stdlog.write(map_mali2seq.Write()) ## add sequence to mali a = alignlib_lite.py_makeAlignatumFromString(cur_record.sequence) a.thisown = 0 new_mali.addAlignatum(a, map_mali2seq, 1, 1, 1, 1, 1) id = cur_record.title mali.mIdentifiers.append(id) mali.mMali[id] = Mali.AlignedString( id, 0, len(cur_record.sequence), new_mali.getRow(new_mali.getWidth() - 1).getString()) # substitute for x in range(old_length): mali.mMali[mali.mIdentifiers[x]].mString = new_mali.getRow( x).getString() mali.writeToFile(sys.stdout, format=options.output_format) E.Stop()