[Biopython-dev] [Bug 3069] Support for EMBL-like files from IMGT

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3069





------- Comment #22 from biopython-bugzilla at maubp.freeserve.co.uk  2010-05-18 18:26 EST -------
(In reply to comment #21)
> (In reply to comment #19)
> 
> > Sorry - I pasted the wrong URL, I mean here:
> > http://github.com/peterjc/biopython/tree/seqio-imgt
> 
> I'm still not sure where you integrated the regular expression.

File Bio/GenBank/Scanner, this commit:
http://github.com/peterjc/biopython/commit/a41db092a40542944158278f2cc26517cd464b60

> > I've found an even worse example of partial location example from
> > http://imgt.cines.fr/download/LIGM-DB/imgt.dat.Z
> > 
> > ID   M97158 IMGT/LIGM annotation : keyword level; RNA; ROD; 1093 BP.
> > XX
> >
> > ...
> > 
> > You can see the original at EMBL,
> > http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&id=M97158&Submit=Go
> > 
> > Or in GenBank format at the NCBI,
> > http://www.ncbi.nlm.nih.gov/nuccore/200865
> 
> That is awful!  And there is no excuse for it either, as they should've just
> taken the coords from EMBL.  I feel as though we should leave these problems
> as errors, and have IMGT fix them. 

In this case (and the other locations with missing text) there is no good work
around so I would agree - get the IMGT to fix them.


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