Re: [Biopython] Fw: Developing a wrapper for EBI dbfetch
有賀淳/Jun Aruga <[email protected]> Sun, 20 Aug 2017 13:12:45 +0200
| Newsgroups | gmane.comp.python.bio.devel,gmane.comp.python.bio.general |
|---|---|
| Message-ID | <CADfndDdFu1OzBp0+o1K9mgTxyLXt=LE=--VvArRg3Tw9NzVCOA@mail.gmail.com> |
--===============8995328066325460971== Content-Type: multipart/alternative; boundary="94eb2c1880241352b105572d7167" --94eb2c1880241352b105572d7167 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Peter, Right now I commented. :) Jun On Wed, Aug 16, 2017 at 11:00 AM, Peter Cock <[email protected]> wrote: > Thanks - we can wait :) > > Peter > > On Wed, Aug 16, 2017 at 12:34 AM, =E6=9C=89=E8=B3=80=E6=B7=B3/Jun Aruga <= [email protected]> wrote: > > Great, > > I want to comment this weekend, if it will have not been merged at that > time > > yet. > > > > Jun > > > > On Tue, Aug 15, 2017 at 5:39 PM, Peter Cock <[email protected]> > > wrote: > >> > >> Would anyone like to comment on Francesco's pull request: > >> > >> https://github.com/biopython/biopython/pull/1298 > >> > >> This is to add a wrapper for EBI's dbfetch, originally logged as: > >> > >> https://github.com/biopython/biopython/issues/443 > >> > >> Thanks, > >> > >> Peter > >> > >> On Wed, Jun 21, 2017 at 12:06 PM, Peter Cock <[email protected]= m > > > >> wrote: > >> > CC biopython-dev for the module naming in particular. > >> > > >> > General feedback or ideas about supporting the EBI's web-interface > >> > (their REST API, similar to the NCBI's Entrez utilities, or TogoWS) > >> > are welcome here or on the GitHub issue: > >> > > >> > https://github.com/biopython/biopython/issues/443 > >> > > >> > Peter > >> > > >> > On Wed, Jun 21, 2017 at 11:25 AM, Francesco Gastaldello (Staff) > >> > <[email protected]> wrote: > >> >> > >> >> Hi all, > >> >> > >> >> this mail regard the development on my behalf for the dbfetch > wrapper. > >> >> More info on the service are here: > >> >> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch > >> >> > >> >> There is already an issue on the Biopython GitHub (#443) were me an= d > >> >> Peter Cock are discussing how to place the module when it's going t= o > be > >> >> ready. > >> >> > >> >> He mentioned the possibility to place it in Bio/EBI/__init__.py, bu= t > >> >> he's concened that this won't comply with PEP8 guidelines. > >> >> > >> >> Any thoughts about it? > >> >> > >> >> Regards, > >> >> > >> >> Francesco > >> >> > >> >> Dbfetch < EMBL-EBI > >> >> www.ebi.ac.uk > >> >> Dbfetch Help. What is dbfetch? Dbfetch is an abbreviation for > "database > >> >> fetch". Dbfetch provides an easy way to retrieve entries from vario= us > >> >> databases at the EMBL ... > >> _______________________________________________ > >> Biopython-dev mailing list > >> [email protected] > >> http://mailman.open-bio.org/mailman/listinfo/biopython-dev > > > > > > > > > > -- > > Jun Aruga > > > --=20 Jun Aruga --94eb2c1880241352b105572d7167 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div><div>Hi Peter,<br><br></div>Right now I commented. :)= <br><br></div>Jun<br><br></div><div class=3D"gmail_extra"><br><div class=3D= "gmail_quote">On Wed, Aug 16, 2017 at 11:00 AM, Peter Cock <span dir=3D"ltr= "><<a href=3D"mailto:[email protected]" target=3D"_blank">p.j.a.= [email protected]</a>></span> wrote:<br><blockquote class=3D"gmail_quo= te" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"= >Thanks - we can wait :)<br> <span class=3D"HOEnZb"><font color=3D"#888888"><br> Peter<br> </font></span><div class=3D"HOEnZb"><div class=3D"h5"><br> On Wed, Aug 16, 2017 at 12:34 AM, =E6=9C=89=E8=B3=80=E6=B7=B3/Jun Aruga <= ;<a href=3D"mailto:[email protected]">[email protected]</a>> wrote:<br> > Great,<br> > I want to comment this weekend, if it will have not been merged at tha= t time<br> > yet.<br> ><br> > Jun<br> ><br> > On Tue, Aug 15, 2017 at 5:39 PM, Peter Cock <<a href=3D"mailto:p.j.= [email protected]">[email protected]</a>><br> > wrote:<br> >><br> >> Would anyone like to comment on Francesco's pull request:<br> >><br> >> <a href=3D"https://github.com/biopython/biopython/pull/1298" rel= =3D"noreferrer" target=3D"_blank">https://github.com/biopython/<wbr>biopyth= on/pull/1298</a><br> >><br> >> This is to add a wrapper for EBI's dbfetch, originally logged = as:<br> >><br> >> <a href=3D"https://github.com/biopython/biopython/issues/443" rel= =3D"noreferrer" target=3D"_blank">https://github.com/biopython/<wbr>biopyth= on/issues/443</a><br> >><br> >> Thanks,<br> >><br> >> Peter<br> >><br> >> On Wed, Jun 21, 2017 at 12:06 PM, Peter Cock <<a href=3D"mailto= :[email protected]">[email protected]</a>><br> >> wrote:<br> >> > CC biopython-dev for the module naming in particular.<br> >> ><br> >> > General feedback or ideas about supporting the EBI's web-= interface<br> >> > (their REST API, similar to the NCBI's Entrez utilities, = or TogoWS)<br> >> > are welcome here or on the GitHub issue:<br> >> ><br> >> > <a href=3D"https://github.com/biopython/biopython/issues/443"= rel=3D"noreferrer" target=3D"_blank">https://github.com/biopython/<wbr>bio= python/issues/443</a><br> >> ><br> >> > Peter<br> >> ><br> >> > On Wed, Jun 21, 2017 at 11:25 AM, Francesco Gastaldello (Staf= f)<br> >> > <<a href=3D"mailto:[email protected]">f.gastaldel= [email protected]</a>> wrote:<br> >> >><br> >> >> Hi all,<br> >> >><br> >> >> this mail regard the development on my behalf for the dbf= etch wrapper.<br> >> >> More info on the service are here:<br> >> >> <a href=3D"http://www.ebi.ac.uk/Tools/dbfetch/dbfetch" re= l=3D"noreferrer" target=3D"_blank">http://www.ebi.ac.uk/Tools/<wbr>dbfetch/= dbfetch</a><br> >> >><br> >> >> There is already an issue on the Biopython GitHub (#443) = were me and<br> >> >> Peter Cock are discussing how to place the module when it= 's going to be<br> >> >> ready.<br> >> >><br> >> >> He mentioned the possibility to place it in Bio/EBI/__ini= t__.py, but<br> >> >> he's concened that this won't comply with PEP8 gu= idelines.<br> >> >><br> >> >> Any thoughts about it?<br> >> >><br> >> >> Regards,<br> >> >><br> >> >> Francesco<br> >> >><br> >> >> Dbfetch < EMBL-EBI<br> >> >> <a href=3D"http://www.ebi.ac.uk" rel=3D"noreferrer" targe= t=3D"_blank">www.ebi.ac.uk</a><br> >> >> Dbfetch Help. What is dbfetch? Dbfetch is an abbreviation= for "database<br> >> >> fetch". Dbfetch provides an easy way to retrieve ent= ries from various<br> >> >> databases at the EMBL ...<br> >> ______________________________<wbr>_________________<br> >> Biopython-dev mailing list<br> >> <a href=3D"mailto:[email protected]">Biopython-de= [email protected]<wbr>bio.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/<wbr>= mailman/listinfo/biopython-dev</a><br> ><br> ><br> ><br> ><br> > --<br> > Jun Aruga<br> ><br> </div></div></blockquote></div><br><br clear=3D"all"><br>-- <br><div class= =3D"gmail_signature" data-smartmail=3D"gmail_signature"><div dir=3D"ltr">Ju= n Aruga<div><br></div></div></div> </div> --94eb2c1880241352b105572d7167-- --===============8995328066325460971== 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 --===============8995328066325460971==--