[Biopython] Is this a valid genbank record?

[Peter Cock]

On Wed, Jan 18, 2012 at 10:14 AM, Michael Thon <mike.thon at gmail.com> wrote:
> Does anyone know if these GenBank records are valid:
>
> http://www.ncbi.nlm.nih.gov/protein/323463153
> http://www.ncbi.nlm.nih.gov/protein/93279336
>
> ...because biopython raised an exception when trying to parse them.  They have weird feature locations:
>
>     Het             join(bond(127),bond(127),bond(130),bond(130),bond(138),
>                     bond(138),bond(139),bond(138))
>
>
> thanks
> Mike

See also: http://www.bioperl.org/wiki/BioPerl_Locations#bond.28location.2Clocation...location.29

The use of "bond" in a feature location isn't described in the official
GenBank/EMBL/DDBJ Feature Table definition, but that is aimed at
nucleotide sequences only. I'm unaware of an official documentation
on GenPept variations.

Being practical we'd better update the parser to cope with it, even
though it does seem to be a rare corner case.

I'd have to go back and check, but I suspect prior to the parser rewrite
back in Biopython 1.55 (released August 2011) we might have allowed
for this.

Are you happy to test an updated parser?

Peter