Re: Adding overall coverage to blast-xml

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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 <[email protected]> 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 <[email protected]> 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
> > [email protected]
> > http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>

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<div dir=3D"ltr"><div>It is indeed qcovs, I was stuck using XML, didn&#39;t=
 investigate that before. I haven&#39;t looked into the SearchIO version ye=
t, but I assume it won&#39;t be more difficult to implement there so I&#39;=
m happy to commit to that.<br></div><div><br></div><div>John</div></div><di=
v class=3D"gmail_extra"><br><div class=3D"gmail_quote">On 11 September 2017=
 at 21:14, Peter Cock <span dir=3D"ltr">&lt;<a href=3D"mailto:p.j.a.cock@go=
oglemail.com" target=3D"_blank">[email protected]</a>&gt;</span> wr=
ote:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border=
-left:1px #ccc solid;padding-left:1ex">Hi John, CC Bow,<br>
<br>
Is this information in any of the BLAST output formats?<br>
<br>
I suspect you are talking about recreating one or more<br>
of the coverage fields which can be requested in the<br>
BLAST csv or tabular output files formats? i.e. qcovs<br>
or qcovhsp perhaps?<br>
<br>
If so, I can see a rational for computing this for the<br>
BLAST XML parsing... although given we&#39;d like to<br>
push people towards SearchIO (which supports the<br>
BLAST tabular format as well), doing it there might<br>
make more sense than in NCBIXML?<br>
<br>
Peter<br>
<div><div class=3D"h5"><br>
On Mon, Sep 11, 2017 at 5:40 PM, John T &lt;<a href=3D"mailto:jaytee00@gmai=
l.com">[email protected]</a>&gt; wrote:<br>
&gt; Hi all,<br>
&gt;<br>
&gt; I&#39;ve written a script that calculates the overall coverage for all=
 HSP in an<br>
&gt; alignment, like that given on the BLAST homepage. Would it make sense =
to add<br>
&gt; this to Bio.Blast.Record.Alignment (and/or the BlastIO equivalent)? It=
&#39;s not<br>
&gt; something that&#39;s explicitly defined in the XML and so may be out o=
f scope,<br>
&gt; but it is something that&#39;s given in the website version of BLAST r=
esults so<br>
&gt; people might reasonably expect it to be there. I&#39;d add it as a @pr=
operty so<br>
&gt; it as only calculated when required.<br>
&gt;<br>
&gt; I&#39;ve never tried contributing to an open source project before so =
I didn&#39;t<br>
&gt; want to dive in and do something stupid.<br>
&gt;<br>
&gt; Cheers,<br>
&gt; John<br>
&gt;<br>
&gt;<br>
</div></div>&gt; ______________________________<wbr>_________________<br>
&gt; Biopython-dev mailing list<br>
&gt; <a href=3D"mailto:[email protected]">Biopython-dev@ma=
ilman.open-<wbr>bio.org</a><br>
&gt; <a href=3D"http://mailman.open-bio.org/mailman/listinfo/biopython-dev"=
 rel=3D"noreferrer" target=3D"_blank">http://mailman.open-bio.org/<wbr>mail=
man/listinfo/biopython-dev</a><br>
</blockquote></div><br></div>

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