[Biopython-dev] [Bug 3175] Caret in genbank files leads to GenBank Parser crash in Biopython 1.54

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http://bugzilla.open-bio.org/show_bug.cgi?id=3175





------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2011-02-04 12:43 EST -------
(In reply to comment #3)
> Hi Peter,
> Thanks for the quick reply. I originally encountered the caret in the GenBank
> entry for the chromosome II assembly of the human genome (accession number
> NT_022221.13, downloaded from NCBI's FTP site yesterday); it can be found at
> the very end of the annotation, for the V_segments/CDS of the IGKV2-40 gene
> e.g.      CDS  complement(<68451760..68452072^68452073). I suspect that it is
> rare, because I parsed through the complete sequences of 15 other chromosomes
> before my program crashed. Hope that helps.
> Cheers,
> Aaron
> 


Where on the FTP site? Its a big place and I don't work with human genomes...

Looking via the Entrez website, it seems NT_022221.13 is only 3519312bp,
so this can't match the GenBank file you are looking at:

http://www.ncbi.nlm.nih.gov/nuccore/NT_022221.13?report=gbwithparts

Thanks,

Peter


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