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 convertMali2Alignlib(mali): '''convert a multiple alignment of type :class:`Mali` into an alignlib_lite.py_multiple alignment object. ''' import alignlib_lite m = alignlib_lite.py_makeMultipleAlignment() for identifier in mali.getIdentifiers(): a = alignlib_lite.py_makeAlignatum(mali[identifier]) m.add(a) return m
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