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#!/usr/bin/env python
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Peter Maxwell", "Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Peter Maxwell"
__email__ = "pm67nz@gmail.com"
__status__ = "Production"
def PamlParser(f):
d = f.readline().split()
numseqs, seqlen = int(d[0]), int(d[1])
for i in range(numseqs):
seqname = f.readline().strip()
if not seqname:
raise ValueError('Sequence name missing')
currseq = []
length = 0
while length < seqlen:
seq_line = f.readline()
if not seq_line:
raise ValueError('Sequence "%s" is short: %s < %s' %
(seqname, length, seqlen))
seq_line = seq_line.strip()
length += len(seq_line)
currseq.append(seq_line)
yield (seqname, ''.join(currseq))
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