Re: Issue with FASTA reader
Jose Duarte <[email protected]> Fri, 7 Jul 2017 16:32:09 -0700
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <CAHhO=JE4fo0W51WJurkPMwfsCnDLJ=du4omqKFHkGS5PZ5hPwA@mail.gmail.com> |
--===============3610084348683796019== Content-Type: multipart/alternative; boundary="001a1147f9ea6387d70553c2a406" --001a1147f9ea6387d70553c2a406 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Make sure you create your own fork of biojava and then push to it. After that you can do a pull request into the main biojava repository. See https://help.github.com/articles/creating-a-pull-request-from-a-fork/ for more info Jose On Fri, Jul 7, 2017 at 4:27 PM, Rojnuckarin, Dak <[email protected]> wrote: > Hi, > > > > I am trying to commit my branch and got =E2=80=9Cgit-receive-pack not per= mitted=E2=80=9D. > I suspect I need commit privilege for biojava repository. If so, my githu= b > username is arojnuckarin (email: [email protected]). If not, I would > appreciate any help figuring this out. > > > > Thanks, > > dak > > > > *From:* Jose Duarte [mailto:[email protected]] > *Sent:* Thursday, June 1, 2017 10:37 AM > *To:* Rojnuckarin, Dak <[email protected]> > *Cc:* Andreas Prlic <[email protected]>; [email protected] > > *Subject:* Re: [Biojava-l] Issue with FASTA reader > > > > Dear Dak > > > > The best way of fixing it yourself is that you modify the code in your ow= n > github fork (ideally in a branch, not in master) and then submit a pull > request so that your patch can be peer reviewed. > > > > All the best > > > > Jose > > > > > > On Thu, Jun 1, 2017 at 8:25 AM, Rojnuckarin, Dak <[email protected]> > wrote: > > Hello, > > > > Andreas mentioned he created a branch in github to contain my test code: > > > > https://github.com/biojava/biojava/commit/9de8e3633a8d66fc4050f14b2e2168 > 4605cf2f7b > > > > but I have not heard back in a while. > > > > What=E2=80=99s the process/etiquette of getting involved and attempt the = fix > myself? > > > > Thanks, > > dak > > > > *From:* [email protected] [mailto:[email protected]] *On > Behalf Of *Andreas Prlic > *Sent:* Wednesday, April 19, 2017 4:34 PM > *To:* Rojnuckarin, Dak <[email protected]> > *Cc:* [email protected] > *Subject:* Re: [Biojava-l] Issue with FASTA reader > > > > Thanks, Dak. I'll create a branch in git which will contain your test, > then we can take it from there. > > > > Andreas > > > > > > > > On Mon, Apr 17, 2017 at 9:43 AM, Rojnuckarin, Dak <[email protected]> > wrote: > > Hi, > > > > I have a FASTA file that contain one sequence. I initialized FASTA reader > as described in the tutorial, called process() and get one record as > expected. However, if I re-initialized another FASTA reader opening the > same one-record file, called process(1) and null is returned. If I tried = to > read two-record FASTA file, the first process(1) works, but not the secon= d > call to process(1) return null. Based on a superficial glance, it looks > like the if statement at line 194 of FastaReader.java may be the culprit. > > > > Test code attached. > > > > Thanks, > > Dak Rojnuckarin > > Research Informatics > > Amgen > > > > > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://mailman.open-bio.org/mailman/listinfo/biojava-l > > > > > > -- > > ----------------------------------------------------------------------- > Dr. Andreas Prlic > RCSB PDB Protein Data Bank > > Technical & Scientific Team Lead > > University of California, San Diego > > > > Editor Software Section > > PLOS Computational Biology > > > > BioJava Project Lead > ----------------------------------------------------------------------- > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://mailman.open-bio.org/mailman/listinfo/biojava-l > > > --001a1147f9ea6387d70553c2a406 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr">Make sure you create your own fork of biojava and then pus= h to it. After that you can do a pull request into the main biojava reposit= ory.=C2=A0<div><br></div><div>See=C2=A0<a href=3D"https://help.github.com/a= rticles/creating-a-pull-request-from-a-fork/">https://help.github.com/artic= les/creating-a-pull-request-from-a-fork/</a> for more info</div><div><br></= div><div>Jose</div></div><div class=3D"gmail_extra"><br><div class=3D"gmail= _quote">On Fri, Jul 7, 2017 at 4:27 PM, Rojnuckarin, Dak <span dir=3D"ltr">= <<a href=3D"mailto:[email protected]" target=3D"_blank">[email protected]= m</a>></span> wrote:<br><blockquote class=3D"gmail_quote" style=3D"margi= n:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <div lang=3D"EN-US" link=3D"blue" vlink=3D"purple"> <div class=3D"m_3283523428624878936WordSection1"> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d">Hi,<u></u><u></u></span></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d"><u></u>=C2=A0<u></u></span></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d">I am trying to commit my branch and g= ot =E2=80=9Cgit-receive-pack not permitted=E2=80=9D. I suspect I need commi= t privilege for biojava repository. If so, my github username is arojnuckarin (email: <a href=3D"mailto:[email protected]" target=3D"_bl= ank">[email protected]</a>). If not, I would appreciate any help figuring t= his out. <u></u><u></u></span></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d"><u></u>=C2=A0<u></u></span></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d">Thanks,<u></u><u></u></span></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d">dak<u></u><u></u></span></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d"><u></u>=C2=A0<u></u></span></p> <p class=3D"MsoNormal"><b><span style=3D"font-size:11.0pt;font-family:"= ;Calibri",sans-serif">From:</span></b><span style=3D"font-size:11.0pt;= font-family:"Calibri",sans-serif"> Jose Duarte [mailto:<a href=3D= "mailto:[email protected]" target=3D"_blank">[email protected]</a>] <br> <b>Sent:</b> Thursday, June 1, 2017 10:37 AM<br> <b>To:</b> Rojnuckarin, Dak <<a href=3D"mailto:[email protected]" target= =3D"_blank">[email protected]</a>><br> <b>Cc:</b> Andreas Prlic <<a href=3D"mailto:[email protected]" target=3D"= _blank">[email protected]</a>>; <a href=3D"mailto:[email protected]= bio.org" target=3D"_blank">[email protected]</a></span></p><di= v><div class=3D"h5"><br> <b>Subject:</b> Re: [Biojava-l] Issue with FASTA reader<u></u><u></u></div>= </div><p></p><div><div class=3D"h5"> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> <div> <p class=3D"MsoNormal">Dear Dak<u></u><u></u></p> <div> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> </div> <div> <p class=3D"MsoNormal">The best way of fixing it yourself is that you modif= y the code in your own github fork (ideally in a branch, not in master) and= then submit a pull request so that your patch can be peer reviewed.<u></u>= <u></u></p> </div> <div> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> </div> <div> <p class=3D"MsoNormal">All the best<u></u><u></u></p> </div> <div> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> </div> <div> <p class=3D"MsoNormal">Jose<u></u><u></u></p> </div> <div> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> </div> </div> <div> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> <div> <p class=3D"MsoNormal">On Thu, Jun 1, 2017 at 8:25 AM, Rojnuckarin, Dak <= ;<a href=3D"mailto:[email protected]" target=3D"_blank">[email protected]</= a>> wrote:<u></u><u></u></p> <blockquote style=3D"border:none;border-left:solid #cccccc 1.0pt;padding:0i= n 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in"> <div> <div> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d">Hello,</span><u></u><u></u></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d">=C2=A0</span><u></u><u></u></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d">Andreas mentioned he created a branch= in github to contain my test code:</span><u></u><u></u></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d">=C2=A0</span><u></u><u></u></p> <p class=3D"MsoNormal"><a href=3D"https://github.com/biojava/biojava/commit= /9de8e3633a8d66fc4050f14b2e21684605cf2f7b" target=3D"_blank">https://github= .com/biojava/<wbr>biojava/commit/<wbr>9de8e3633a8d66fc4050f14b2e2168<wbr>46= 05cf2f7b</a><u></u><u></u></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d">=C2=A0</span><u></u><u></u></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d">but I have not heard back in a while. </span><u></u><u></u></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d">=C2=A0</span><u></u><u></u></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d">What=E2=80=99s the process/etiquette = of getting involved and attempt the fix myself?</span><u></u><u></u></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d">=C2=A0</span><u></u><u></u></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d">Thanks,</span><u></u><u></u></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d">dak</span><u></u><u></u></p> <p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca= libri",sans-serif;color:#1f497d">=C2=A0</span><u></u><u></u></p> <p class=3D"MsoNormal"><b><span style=3D"font-size:11.0pt;font-family:"= ;Calibri",sans-serif">From:</span></b><span style=3D"font-size:11.0pt;= font-family:"Calibri",sans-serif"> <a href=3D"mailto:[email protected]" target=3D"_blank">andreas.prlic@= gmail.com</a> [mailto:<a href=3D"mailto:[email protected]" target=3D"= _blank">andreas.prlic@gmail.<wbr>com</a>] <b>On Behalf Of </b>Andreas Prlic<br> <b>Sent:</b> Wednesday, April 19, 2017 4:34 PM<br> <b>To:</b> Rojnuckarin, Dak <<a href=3D"mailto:[email protected]" target= =3D"_blank">[email protected]</a>><br> <b>Cc:</b> <a href=3D"mailto:[email protected]" target=3D"_bla= nk">[email protected]</a><br> <b>Subject:</b> Re: [Biojava-l] Issue with FASTA reader</span><u></u><u></u= ></p> <div> <div> <p class=3D"MsoNormal">=C2=A0<u></u><u></u></p> <div> <p class=3D"MsoNormal">Thanks, Dak. I'll create a branch in git which w= ill contain your test, then we can take it from there.<u></u><u></u></p> <div> <p class=3D"MsoNormal">=C2=A0<u></u><u></u></p> </div> <div> <p class=3D"MsoNormal">Andreas<u></u><u></u></p> <div> <p class=3D"MsoNormal">=C2=A0<u></u><u></u></p> </div> <div> <p class=3D"MsoNormal">=C2=A0<u></u><u></u></p> </div> </div> </div> <div> <p class=3D"MsoNormal">=C2=A0<u></u><u></u></p> <div> <p class=3D"MsoNormal">On Mon, Apr 17, 2017 at 9:43 AM, Rojnuckarin, Dak &l= t;<a href=3D"mailto:[email protected]" target=3D"_blank">[email protected]<= /a>> wrote:<u></u><u></u></p> <blockquote style=3D"border:none;border-left:solid #cccccc 1.0pt;padding:0i= n 0in 0in 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0in;margin-= bottom:5.0pt"> <div> <div> <p class=3D"MsoNormal">Hi,<u></u><u></u></p> <p class=3D"MsoNormal">=C2=A0<u></u><u></u></p> <p class=3D"MsoNormal">I have a FASTA file that contain one sequence. I ini= tialized FASTA reader as described in the tutorial, called process() and ge= t one record as expected. However, if I re-initialized another FASTA reader opening the same one-record file, called process(1) a= nd null is returned. If I tried to read two-record FASTA file, the first pr= ocess(1) works, but not the second call to process(1) return null. Based on= a superficial glance, it looks like the if statement at line 194 of FastaReader.java may be the culprit. = <u></u><u></u></p> <p class=3D"MsoNormal">=C2=A0<u></u><u></u></p> <p class=3D"MsoNormal">Test code attached.<u></u><u></u></p> <p class=3D"MsoNormal">=C2=A0<u></u><u></u></p> <p class=3D"MsoNormal">Thanks,<u></u><u></u></p> <p class=3D"MsoNormal">Dak Rojnuckarin<u></u><u></u></p> <p class=3D"MsoNormal">Research Informatics<u></u><u></u></p> <p class=3D"MsoNormal">Amgen<u></u><u></u></p> <p class=3D"MsoNormal">=C2=A0<u></u><u></u></p> <p class=3D"MsoNormal">=C2=A0=C2=A0<u></u><u></u></p> </div> </div> <p class=3D"MsoNormal"><br> ______________________________<wbr>_________________<br> Biojava-l mailing list=C2=A0 -=C2=A0 <a href=3D"mailto:[email protected]= en-bio.org" target=3D"_blank"> [email protected]</a><br> <a href=3D"http://mailman.open-bio.org/mailman/listinfo/biojava-l" target= =3D"_blank">http://mailman.open-bio.org/<wbr>mailman/listinfo/biojava-l</a>= <u></u><u></u></p> </blockquote> </div> <p class=3D"MsoNormal"><br> <br clear=3D"all"> <u></u><u></u></p> <div> <p class=3D"MsoNormal">=C2=A0<u></u><u></u></p> </div> <p class=3D"MsoNormal">-- <u></u><u></u></p> <div> <div> <div> <div> <p class=3D"MsoNormal">------------------------------<wbr>-----------------= -------------<wbr>-----------<br> Dr. Andreas Prlic<br> RCSB PDB Protein Data Bank<u></u><u></u></p> </div> <div> <p class=3D"MsoNormal">Technical & Scientific Team Lead<u></u><u></u></= p> </div> <div> <p class=3D"MsoNormal">University of California, San Diego<u></u><u></u></p= > <div> <p class=3D"MsoNormal">=C2=A0<u></u><u></u></p> </div> <div> <p class=3D"MsoNormal">Editor Software Section=C2=A0<u></u><u></u></p> <div> <p class=3D"MsoNormal">PLOS Computational Biology<u></u><u></u></p> <div> <div> <div> <p class=3D"MsoNormal">=C2=A0<u></u><u></u></p> </div> <div> <p class=3D"MsoNormal">BioJava Project Lead<br> ------------------------------<wbr>------------------------------<wbr>-----= ------<u></u><u></u></p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <p class=3D"MsoNormal"><br> ______________________________<wbr>_________________<br> Biojava-l mailing list=C2=A0 -=C2=A0 <a href=3D"mailto:[email protected]= en-bio.org" target=3D"_blank">[email protected]</a><br> <a href=3D"http://mailman.open-bio.org/mailman/listinfo/biojava-l" target= =3D"_blank">http://mailman.open-bio.org/<wbr>mailman/listinfo/biojava-l</a>= <u></u><u></u></p> </blockquote> </div> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> </div> </div></div></div> </div> </blockquote></div><br></div> --001a1147f9ea6387d70553c2a406-- --===============3610084348683796019== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Biojava-l mailing list - [email protected] http://mailman.open-bio.org/mailman/listinfo/biojava-l --===============3610084348683796019==--