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

Peter Cock p.j.a.cock at googlemail.com
Mon Sep 11 20:14:14 UTC 2017

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?


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
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