[BioPython] GenBank parser

[Leighton Pritchard]

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Hi,

I've noticed an oddity in the GenBank FeatureParser (CVS installation
19/4).  While parsing the Salmonella typhi file NC_003198.gbk, my way of
dealing with 'gene' tags fell over.  This turned out to be because the
GenBank file contains entries with valueless tags such as /partial and
/pseudo.  The current parser concatenates these tags with the following
tag, e.g for:

~     CDS             1449249..1450391
~                     /partial
~                     /gene="fdnG"
~                     /note="Similar to part of Escherichia coli formate
~                     dehydrogenase, nitrate-inducible, major subunit fdnG
~                     SW:FDNG_ECOLI (P24183; P78261) (1015 aa) fasta scores:
~                     E(): 0, 94.4% id in 376 aa"
~                     /pseudo
~                     /codon_start=1
~                     /transl_table=11

it returns a set of qualifiers which include the tags "partial gene" and
"pseudo codon_start".  This probably isn't what was intended by the
authors ;)

I haven't got a fix for the parser, but my workaround in the code was:

##################

qualifiers = cds.qualifiers             # Shorthand for qualifiers
# We need to account for use of qualifiers, e.g. in
# NC_003198.gbk, the /partial and /pseudo tags often have no
# associated value - the BioPython GenBank feature parser lumps the
# two together into a single tag, e.g. 'partial gene' and
# 'pseudo codon_start'.  This buggers up our processing below,
# so the solution is to split tags by the ' ' space character,
# and add a qualifier comprising only the last item in the
# resulting list
for key in qualifiers.keys():
~    if key.count(' '):
~        qualifiers[key.split(' ')[-1]] = qualifiers[key]

###################

...I wasn't bothered about the partial or pseudo tags for my script

- --
Dr Leighton Pritchard AMRSC
D104, PPI, Scottish Crop Research Institute
Invergowrie, Dundee, DD2 5DA, Scotland, UK
E: lpritc at scri.sari.ac.uk	W: http://bioinf.scri.sari.ac.uk/index.shtml
T: +44 (0)1382 568579		F: +44 (0)1382 568578
PGP key FEFC205C: GPG key E58BA41B: http://www.keyserver.net
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