[Biopython-dev] Adding overall coverage to blast-xml

[John T]

It is indeed qcovs, I was stuck using XML, didn't investigate that before.
I haven't looked into the SearchIO version yet, but I assume it won't be
more difficult to implement there so I'm happy to commit to that.

John

On 11 September 2017 at 21:14, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> Hi John, CC Bow,
>
> Is this information in any of the BLAST output formats?
>
> I suspect you are talking about recreating one or more
> of the coverage fields which can be requested in the
> BLAST csv or tabular output files formats? i.e. qcovs
> or qcovhsp perhaps?
>
> If so, I can see a rational for computing this for the
> BLAST XML parsing... although given we'd like to
> push people towards SearchIO (which supports the
> BLAST tabular format as well), doing it there might
> make more sense than in NCBIXML?
>
> Peter
>
> On Mon, Sep 11, 2017 at 5:40 PM, John T <jaytee00 at gmail.com> wrote:
> > Hi all,
> >
> > I've written a script that calculates the overall coverage for all HSP
> in an
> > alignment, like that given on the BLAST homepage. Would it make sense to
> add
> > this to Bio.Blast.Record.Alignment (and/or the BlastIO equivalent)? It's
> not
> > something that's explicitly defined in the XML and so may be out of
> scope,
> > but it is something that's given in the website version of BLAST results
> so
> > people might reasonably expect it to be there. I'd add it as a @property
> so
> > it as only calculated when required.
> >
> > I've never tried contributing to an open source project before so I
> didn't
> > want to dive in and do something stupid.
> >
> > Cheers,
> > John
> >
> >
> > _______________________________________________
> > Biopython-dev mailing list
> > Biopython-dev at mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython-dev/attachments/20170911/eecde00c/attachment.html>