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#!/usr/bin/env python
#from xml.dom.minidom import parse as xmlparse
from cogent.core import annotation, moltype
__author__ = "Matthew Wakefield"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Matthew Wakefield", "Peter Maxwell", "Gavin Huttley",
"Rob Knight"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Matthew Wakefield"
__email__ = "matthew.wakefield@anu.edu.au"
__status__ = "Production"
def TinyseqParser(doc):
for record in doc.getElementsByTagName('TSeq'):
raw_seq = record.getElementsByTagName(
'TSeq_sequence')[0].childNodes[0].nodeValue
name = record.getElementsByTagName(
'TSeq_accver')[0].childNodes[0].nodeValue
#cast as string to de-unicode
raw_string = str(raw_seq).upper()
name=str(name)
if record.getElementsByTagName(
'TSeq_seqtype')[0].getAttribute('value') == u'protein':
alphabet = moltype.PROTEIN
else:
alphabet = moltype.DNA
seq = alphabet.makeSequence(raw_string, Name=name)
seq.addAnnotation(annotation.Feature, "genbank_id", name, [(0,len(seq))])
organism = str(record.getElementsByTagName(
'TSeq_orgname')[0].childNodes[0].nodeValue)
seq.addAnnotation(annotation.Feature, "organism", organism, [(0,len(seq))])
yield (name, seq)
def parse(*args):
return TinyseqParser(*args).next()[1]
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