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

Peter Cock p.j.a.cock at googlemail.com
Tue Sep 12 09:28:58 UTC 2017

Hi John,

At least if its qcovs (or qcovhsp) there is a clear base value
from the NCBI code for guidance and conformance testing.

I'm still a little uncomfortable with a parser inferring to many
advanced values like this, but will defer to Bow as the
SearchIO author to comment on this might fit into his
object model (e.g. does this have parallels in the other
supported formats?).

(I'm pretty sure this general topic has come up in the past,
but couldn't immediately find an old issue or email thread.)



On Mon, Sep 11, 2017 at 10:02 PM, John T <jaytee00 at gmail.com> wrote:

> 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
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