Hi, you could try this:
def parse(self, ifile):
id=""
seq=""
for line in open(ifile, 'r'):
if '>'==line[0]:
if id!="" and len(seq)>0:
yield id,seq
seq = ""
id=line[1:].strip("\n")
elif id!="":
for word in line.split():
seq += word
if id!="" and len(seq)>0:
yield id,seq
for id, seq in parse("some.fa"):
print "%s \n %s" %(id, seq)
Its adapted from the fasta parser in PyGr.
>From what I understand biopython isnt very active and I think theres a
re-factor of it going on at the moment in the form of corebio.
Hope this helps;
Thanks
Nathan
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