def muscle(self):
"""Do an alignment with muscle.
Its all done in memory -- no files are written.
An alignment object is returned.
The order of the sequences in the new alignment is made to be
the same as the order in self.
"""
flob = cStringIO.StringIO()
self.writeFasta(fName=flob)
p = Popen(["muscle"], stdin=PIPE, stdout=PIPE, stderr=PIPE)
ret = p.communicate(input=flob.getvalue())
flob.close()
try:
a = func.readAndPop(ret[0])
except P4Error:
print ret
raise P4Error("Something didn't work ...")
a.makeSequenceForNameDict()
newSequenceList = []
for sSelf in self.sequences:
newSequenceList.append(a.sequenceForNameDict[sSelf.name])
a.sequences = newSequenceList
return a
def clustalo(self):
"""Do an alignment with clustalo.
Its all done in memory -- no files are written.
An alignment object is returned.
The order of the sequences in the new alignment is made to be
the same as the order in self.
"""
flob = cStringIO.StringIO()
self.writeFasta(fName=flob)
p = Popen(["clustalo", "-i", "-"], stdin=PIPE, stdout=PIPE, stderr=PIPE)
ret = p.communicate(input=flob.getvalue())
# ret = p.communicate()
if ret[1]:
print ret
raise P4Error("clustalo() Something wrong here ...")
flob.close()
a = func.readAndPop(ret[0])
a.makeSequenceForNameDict()
newSequenceList = []
for sSelf in self.sequences:
newSequenceList.append(a.sequenceForNameDict[sSelf.name])
a.sequences = newSequenceList
return a
def clustalo(self):
"""Do an alignment with clustalo.
Its all done in memory -- no files are written.
An alignment object is returned.
The order of the sequences in the new alignment is made to be
the same as the order in self.
"""
flob = cStringIO.StringIO()
self.writeFasta(fName=flob)
p = Popen(["clustalo", "-i", "-"],
stdin=PIPE,
stdout=PIPE,
stderr=PIPE)
ret = p.communicate(input=flob.getvalue())
#ret = p.communicate()
#print ret
flob.close()
a = func.readAndPop(ret[0])
a.makeSequenceForNameDict()
newSequenceList = []
for sSelf in self.sequences:
newSequenceList.append(a.sequenceForNameDict[sSelf.name])
a.sequences = newSequenceList
return a