Re: Adding overall coverage to blast-xml
Peter Cock <[email protected]> Tue, 12 Sep 2017 10:28:58 +0100
| Newsgroups | gmane.comp.python.bio.devel |
|---|---|
| Message-ID | <CAKVJ-_4xj=kyhB5++xVnMnnSiTUkJ8HszB_SJgnMBG83+m1=dg@mail.gmail.com> |
--===============6979413607535673795== Content-Type: multipart/alternative; boundary="94eb2c06c3a44c95400558faaca2" --94eb2c06c3a44c95400558faaca2 Content-Type: text/plain; charset="UTF-8" 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.) Bow? Peter On Mon, Sep 11, 2017 at 10:02 PM, John T <[email protected]> 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 <[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 >> > > --94eb2c06c3a44c95400558faaca2 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>Hi John,</div><div><br></div><div>At least if its qco= vs (or qcovhsp) there is a clear base value<div>from the NCBI code for guid= ance and conformance testing.</div></div><div><br></div><div>I'm still = a little uncomfortable with a parser inferring to many<br></div><div>advanc= ed values like this, but will defer to Bow as the</div><div>SearchIO author= to comment on this might fit into his</div><div>object model (e.g. does th= is have parallels in the other</div><div>supported formats?).</div><div><br= ></div><div><div>(I'm pretty sure this general topic has come up in the= past,</div><div>but couldn't immediately find an old issue or email th= read.)</div></div><div><br></div><div>Bow?</div><div><br></div><div>Peter</= div></div><div class=3D"gmail_extra"><br><div class=3D"gmail_quote">On Mon,= Sep 11, 2017 at 10:02 PM, John T <span dir=3D"ltr"><<a href=3D"mailto:j= [email protected]" target=3D"_blank">[email protected]</a>></span> wrot= e:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-l= eft:1px #ccc solid;padding-left:1ex"><div dir=3D"ltr"><div>It is indeed qco= vs, 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 d= ifficult to implement there so I'm happy to commit to that.<span class= =3D"HOEnZb"><font color=3D"#888888"><br></font></span></div><span class=3D"= HOEnZb"><font color=3D"#888888"><div><br></div><div>John</div></font></span= ></div><div class=3D"HOEnZb"><div class=3D"h5"><div class=3D"gmail_extra"><= br><div class=3D"gmail_quote">On 11 September 2017 at 21:14, Peter Cock <sp= an dir=3D"ltr"><<a href=3D"mailto:[email protected]" target=3D"_= blank">[email protected]</a>></span> wrote:<br><blockquote class= =3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padd= ing-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'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"m_9172762734742828488h5"><br> On Mon, Sep 11, 2017 at 5:40 PM, John T <<a href=3D"mailto:jaytee00@gmai= l.com" target=3D"_blank">[email protected]</a>> wrote:<br> > Hi all,<br> ><br> > I've written a script that calculates the overall coverage for all= HSP in an<br> > alignment, like that given on the BLAST homepage. Would it make sense = to add<br> > this to Bio.Blast.Record.Alignment (and/or the BlastIO equivalent)? It= 's not<br> > something that's explicitly defined in the XML and so may be out o= f scope,<br> > but it is something that's given in the website version of BLAST r= esults so<br> > people might reasonably expect it to be there. I'd add it as a @pr= operty so<br> > it as only calculated when required.<br> ><br> > I've never tried contributing to an open source project before so = I didn't<br> > want to dive in and do something stupid.<br> ><br> > Cheers,<br> > John<br> ><br> ><br> </div></div>> ______________________________<wbr>_________________<br> > Biopython-dev mailing list<br> > <a href=3D"mailto:[email protected]" target=3D"_blank= ">[email protected]<wbr>.org</a><br> > <a href=3D"http://mailman.open-bio.org/mailman/listinfo/biopython-dev"= rel=3D"noreferrer" target=3D"_blank">http://mailman.open-bio.org/ma<wbr>il= man/listinfo/biopython-dev</a><br> </blockquote></div><br></div> </div></div></blockquote></div><br></div> --94eb2c06c3a44c95400558faaca2-- --===============6979413607535673795== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Biopython-dev mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/biopython-dev --===============6979413607535673795==--