Re: [Biopython] Fw: Developing a wrapper for EBI dbfetch
有賀淳/Jun Aruga <[email protected]> Wed, 16 Aug 2017 01:34:32 +0200
| Newsgroups | gmane.comp.python.bio.devel,gmane.comp.python.bio.general |
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| Message-ID | <CADfndDcpO+CJz97LFuzNZwnypCuxdQqbJ5Gxy1UG308LjhO73g@mail.gmail.com> |
--===============5762771567515705295== Content-Type: multipart/alternative; boundary="f403043618b8b753340556d33818" --f403043618b8b753340556d33818 Content-Type: text/plain; charset="UTF-8" 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]> > 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 and > Peter Cock are discussing how to place the module when it's going to be > ready. > >> > >> He mentioned the possibility to place it in Bio/EBI/__init__.py, but > 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 various > databases at the EMBL ... > _______________________________________________ > Biopython-dev mailing list > [email protected] > http://mailman.open-bio.org/mailman/listinfo/biopython-dev > -- Jun Aruga --f403043618b8b753340556d33818 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div><div>Great,<br></div>I want to comment this weekend, = if it will have not been merged at that time yet.<br><br></div>Jun<br></div= ><div class=3D"gmail_extra"><br><div class=3D"gmail_quote">On Tue, Aug 15, = 2017 at 5:39 PM, Peter Cock <span dir=3D"ltr"><<a href=3D"mailto:p.j.a.c= [email protected]" target=3D"_blank">[email protected]</a>></sp= an> wrote:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;= border-left:1px #ccc solid;padding-left:1ex">Would anyone like to comment o= n Francesco's pull request:<br> <br> <a href=3D"https://github.com/biopython/biopython/pull/1298" rel=3D"norefer= rer" target=3D"_blank">https://github.com/biopython/<wbr>biopython/pull/129= 8</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"norefe= rrer" target=3D"_blank">https://github.com/biopython/<wbr>biopython/issues/= 443</a><br> <br> Thanks,<br> <br> Peter<br> <div class=3D"HOEnZb"><div class=3D"h5"><br> On Wed, Jun 21, 2017 at 12:06 PM, Peter Cock <<a href=3D"mailto:p.j.a.co= [email protected]">[email protected]</a>> 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"n= oreferrer" target=3D"_blank">https://github.com/biopython/<wbr>biopython/is= sues/443</a><br> ><br> > Peter<br> ><br> > On Wed, Jun 21, 2017 at 11:25 AM, Francesco Gastaldello (Staff)<br> > <<a href=3D"mailto:[email protected]">f.gastaldello@dundee= .ac.uk</a>> wrote:<br> >><br> >> Hi all,<br> >><br> >> this mail regard the development on my behalf for the dbfetch wrap= per. More info on the service are here: <a href=3D"http://www.ebi.ac.uk/Too= ls/dbfetch/dbfetch" rel=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 a= nd Peter Cock are discussing how to place the module when it's going to= be ready.<br> >><br> >> He mentioned the possibility to place it in Bio/EBI/__init__.py, b= ut he's concened that this won't comply with PEP8 guidelines.<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" target=3D"_bla= nk">www.ebi.ac.uk</a><br> >> Dbfetch Help. What is dbfetch? Dbfetch is an abbreviation for &quo= t;database fetch". Dbfetch provides an easy way to retrieve entries fr= om various databases at the EMBL ...<br> ______________________________<wbr>_________________<br> Biopython-dev mailing list<br> <a href=3D"mailto:[email protected]">Biopython-dev@mailman= .open-<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> </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> --f403043618b8b753340556d33818-- --===============5762771567515705295== 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 --===============5762771567515705295==--