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 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 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
