[Biopython-dev] More 'fun' with GenBank

[Peter Cock]

On Tue, Jan 15, 2013 at 3:54 PM, Kai Blin
<kai.blin at biotech.uni-tuebingen.de> wrote:
> Hi folks,
>
> as people are hitting my web service with all sorts of wonky GenBank
> files, I've stumbled over another one that throws the GenBank parser off
> track.
>
> The culprit is a SeqFeature with a location line like:
>
>      CDS             join(complement(4093..4338),complement(3876..4011),
>                      complement(3655..3809),complement(3284..3585),
>                      complement(2421..2813),complement(2057..2303))
>
> Now, the way I read the GenBank spec, this is not a valid location line,
> but should instead be a complement() of joins(). Unfortunately, the NCBI
> seems to disagree with its own specs, and put the record into their
> Nucleotide database as CABT02000004, which means that by all practical
> purposes, it _is_ a valid GenBank file and the parser should cope.

That should work - for a while GenBank and EMBL didn't agree about
joins on the complement strand, one did complement(join(a..b,c..d))
and the other join(complement(c..d),complement(a..b)), notice the
order of the sub-regions flips.

> The parser looks at this location and creates a feature on the -1
> strand, from 4092:2303. This is caused by by the feature location
> calculation on
> https://github.com/biopython/biopython/blob/master/Bio/GenBank/__init__.py#L1049
> and the lines after.
>
> In short, we do
>             s = cur_feature.sub_features[0].location.start
>             e = cur_feature.sub_features[-1].location.end
>             cur_feature.location = SeqFeature.FeatureLocation(s, e, strand)

For join feature locations, the sub-feature locations should be fine
but the overall feature location is a bit weird/broken for negative
and mixed strands.

This was one of the things the re-factoring on this branch aimed to
fix, https://github.com/peterjc/biopython/tree/f_loc4/
http://lists.open-bio.org/pipermail/biopython-dev/2012-July/009803.html

I was intending to bring this up again after the next release (which
could be later this month or February 2012), but perhaps it would
be worth doing now?

Peter