[Biopython] error in parseing Gene bank
Peter Cock
p.j.a.cock at googlemail.com
Wed Oct 3 14:42:58 UTC 2012
On Wed, Oct 3, 2012 at 3:39 PM, francesco chiani
<francesco.chiani at gmail.com> wrote:
> Thanks for the replys:
>
> here the gbk file:
>
> LOCUS allele_48659_OTTMUSE00000300743_L1L2_Bact_P 37935 bp
> dna linear UNK
> ACCESSION unknown
> DBSOURCE accession design_id=48659
> COMMENT cassette : L1L2_Bact_P
> COMMENT design_id : 48659
> FEATURES Location/Qualifiers
> ...
As Nick guessed, I think the problem is you have 'dna' (lower case)
in the LOCUS line, rather than 'DNA' (upper case). Where did this
file come from? e.g. What software tool or database made it?
http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord#MoleculeTypeB
In any case, perhaps Biopython could check for 'dna' as well
(as some tools don't seem for obey this bit of the standard)?
Thanks
Peter
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