Re: Sanger sequencing trace files support
Andreas Prlic <[email protected]> Wed, 13 Jul 2016 05:58:11 -0700
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <CALthepyTK+0AtR_pU-zK6N1qhTP7LfUWOs8KgqvT0KS2Zvuhjw@mail.gmail.com> |
--===============1017426707316622587== Content-Type: multipart/alternative; boundary=001a114f1ef21da024053783f0bf --001a114f1ef21da024053783f0bf Content-Type: text/plain; charset=UTF-8 Thanks, I filed this as a feature request for the BioJava 4 series on GitHub. Andreas On Wed, Jul 13, 2016 at 4:10 AM, Peter Cock <[email protected]> wrote: > Hi Jonas, > > Thanks for emailing me that example with an M in the sequence. > Biopython could parse it fine, and having checked our existing > sample test files, this one has K, R and Y bases: > > https://github.com/biopython/biopython/blob/master/Tests/Abi/3730.ab1 > > BioJava would be welcome to use that (double check with > Bow, CC'd, if you need it explicitly under a different licence). > > Regards, > > Peter > > > On Tue, Jul 12, 2016 at 5:41 PM, Peter Cock <[email protected]> > wrote: > > Hi Jonas, > > > > Are you happy to share sample file(s) using IUPAC ambiguity > > codes like M = A or C which could be freely used by BioJava > > and other projects as a test case? > > > > (I'm specifically asking for Biopython as I'm not sure if anyone > > has tried this with our ABI parser) > > > > Thanks, > > > > Peter > > > > On Tue, Jul 12, 2016 at 4:26 PM, Jonas Dehairs <[email protected]> > wrote: > >> The 4.2 API currently does not have methods for importing and > >> handeling Sanger sequencing files (ABI, SCF). I'm currently resorting > >> to the legacy classes in 1.9.1 (ChromatogramFactory and Chromatogram). > >> > >> ChromatogramFactory only supports Sanger trace files with standard > >> ATGCN characters. It throws a > >> UnsupportedChromatogramFormatException upon reading Sanger files with > >> IUPAC Ambiguity Codes (for example M = A or C). Even if I would just > >> like to access the traces and ignore the base calls, this is > >> impossible with the current implementation since we can't even open > >> the file if it contains Ambiguity codes. > >> > >> On a side note, I have been getting more and more questions from users > >> why they can't open their Sanger sequencing files (in my program that > >> uses BioJava). I think the popularity of CRISPR and the > >> characterization of CRISPR KO clones (which is likely to result in > >> heterozygous base calls) is increasing the number of people that have > >> these IUPAC Ambiguity Sanger files. > >> > >> For now, I tell people to go back to the Sanger sequencing software > >> that exports the ABI or SCF files and disable IUPAC Ambiguity in the > >> export options. In that case the base calling algorithm just picks the > >> strongest signals in case of ambiguity and sticks to standard ATGCN > >> characters. > >> > >> Anyway, I am requesting the addition of the Chromatogram classes to > >> the new API with support for opening files if they contain UPAC > >> Ambiguity Codes. > >> > >> Thank you for this useful API, > >> _______________________________________________ > >> Biojava-l mailing list - [email protected] > >> http://mailman.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ > Biojava-l mailing list - [email protected] > http://mailman.open-bio.org/mailman/listinfo/biojava-l > --001a114f1ef21da024053783f0bf Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr">Thanks,<div><br></div><div>I filed this as a feature reque= st for the BioJava 4 series on GitHub.</div><div><br></div><div>Andreas</di= v><div class=3D"gmail_extra"><br><div class=3D"gmail_quote">On Wed, Jul 13,= 2016 at 4:10 AM, Peter Cock <span dir=3D"ltr"><<a href=3D"mailto:p.j.a.= [email protected]" target=3D"_blank">[email protected]</a>></s= pan> wrote:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex= ;border-left:1px #ccc solid;padding-left:1ex">Hi Jonas,<br> <br> Thanks for emailing me that example with an M in the sequence.<br> Biopython could parse it fine, and having checked our existing<br> sample test files, this one has K, R and Y bases:<br> <br> <a href=3D"https://github.com/biopython/biopython/blob/master/Tests/Abi/373= 0.ab1" rel=3D"noreferrer" target=3D"_blank">https://github.com/biopython/bi= opython/blob/master/Tests/Abi/3730.ab1</a><br> <br> BioJava would be welcome to use that (double check with<br> Bow, CC'd, if you need it explicitly under a different licence).<br> <br> Regards,<br> <br> Peter<br> <div class=3D"HOEnZb"><div class=3D"h5"><br> <br> On Tue, Jul 12, 2016 at 5:41 PM, Peter Cock <<a href=3D"mailto:p.j.a.coc= [email protected]">[email protected]</a>> wrote:<br> > Hi Jonas,<br> ><br> > Are you happy to share sample file(s) using IUPAC ambiguity<br> > codes like M =3D A or C which could be freely used by BioJava<br> > and other projects as a test case?<br> ><br> > (I'm specifically asking for Biopython as I'm not sure if anyo= ne<br> > has tried this with our ABI parser)<br> ><br> > Thanks,<br> ><br> > Peter<br> ><br> > On Tue, Jul 12, 2016 at 4:26 PM, Jonas Dehairs <<a href=3D"mailto:j= [email protected]">[email protected]</a>> wrote:<br> >> The 4.2 API currently does not have methods for importing and<br> >> handeling Sanger sequencing files (ABI, SCF). I'm currently re= sorting<br> >> to the legacy classes in 1.9.1 (ChromatogramFactory and Chromatogr= am).<br> >><br> >> ChromatogramFactory only supports Sanger trace files with standard= <br> >> ATGCN characters. It throws a<br> >> UnsupportedChromatogramFormatException upon reading Sanger files w= ith<br> >> IUPAC Ambiguity Codes (for example M =3D A or C). Even if I would = just<br> >> like to access the traces and ignore the base calls, this is<br> >> impossible with the current implementation since we can't even= open<br> >> the file if it contains Ambiguity codes.<br> >><br> >> On a side note, I have been getting more and more questions from u= sers<br> >> why they can't open their Sanger sequencing files (in my progr= am that<br> >> uses BioJava). I think the popularity of CRISPR and the<br> >> characterization of CRISPR KO clones (which is likely to result in= <br> >> heterozygous base calls) is increasing the number of people that h= ave<br> >> these IUPAC Ambiguity Sanger files.<br> >><br> >> For now, I tell people to go back to the Sanger sequencing softwar= e<br> >> that exports the ABI or SCF files and disable IUPAC Ambiguity in t= he<br> >> export options. In that case the base calling algorithm just picks= the<br> >> strongest signals in case of ambiguity and sticks to standard ATGC= N<br> >> characters.<br> >><br> >> Anyway, I am requesting the addition of the Chromatogram classes t= o<br> >> the new API with support for opening files if they contain UPAC<br= > >> Ambiguity Codes.<br> >><br> >> Thank you for this useful API,<br> >> _______________________________________________<br> >> Biojava-l mailing list=C2=A0 -=C2=A0 <a href=3D"mailto:Biojava-l@m= ailman.open-bio.org">[email protected]</a><br> >> <a href=3D"http://mailman.open-bio.org/mailman/listinfo/biojava-l"= rel=3D"noreferrer" target=3D"_blank">http://mailman.open-bio.org/mailman/l= istinfo/biojava-l</a><br> _______________________________________________<br> Biojava-l mailing list=C2=A0 -=C2=A0 <a href=3D"mailto:[email protected]= en-bio.org">[email protected]</a><br> <a href=3D"http://mailman.open-bio.org/mailman/listinfo/biojava-l" rel=3D"n= oreferrer" target=3D"_blank">http://mailman.open-bio.org/mailman/listinfo/b= iojava-l</a><br> </div></div></blockquote></div><br><br clear=3D"all"><div><br></div> </div></div> --001a114f1ef21da024053783f0bf-- --===============1017426707316622587== 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 --===============1017426707316622587==--