Re: Documentation, tutorials and cookbook about pairwise sequence alignment
Andrea Battistelli <[email protected]> Wed, 25 May 2016 12:49:50 +0200
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <CANDNoNS+N-=xrLuQGK7xDhK6BGoSNfxHgz+FpNg1toJsimrMDQ@mail.gmail.com> |
--===============8806665391984828344== Content-Type: multipart/alternative; boundary=001a113b18e8cfdc5c0533a86e86 --001a113b18e8cfdc5c0533a86e86 Content-Type: text/plain; charset=UTF-8 Ok understood, sorry. Now it works, thank you Andreas. 2016-05-24 20:30 GMT+02:00 Andreas Prlic <[email protected]>: > Hi Andreas, > > please don't mail me directly with questions, but keep them on the list, > for the benefit of other users who might be in the same situation. > > You are right, the signature of SubstitutionMatrix has changed at some > point in the past. Try this: > > SubstitutionMatrix<AminoAcidCompound> matrix = SubstitutionMatrixHelper.getBlosum65(); > > > There is also another example in the "demo" package of the alignment module, that you could take a look at. > > About the tutorial: When you have the basics figured out, any contributions/pull requests to improve the tutorial will be welcome! ;-) > > A > > > > > On Tue, May 24, 2016 at 5:51 AM, Andrea Battistelli < > [email protected]> wrote: > >> Hi Andreas. >> >> I have seen the codes in the page you suggested me. >> I have encountered some errors about: >> >> *import org.biojava.nbio.alignment.template.SequencePair;* >> >> >> *import org.biojava.nbio.alignment.template.SubstitutionMatrix;* >> Regarding all the other imports, there are not problems. >> Indeed in the code I have errors in this part: >> >> *SubstitutionMatrix<AminoAcidCompound> matrix = new >> SimpleSubstitutionMatrix<AminoAcidCompound>();* >> *List<SequencePair<ProteinSequence, AminoAcidCompound>> alig = >> Alignments.getAllPairsAlignments(lst,* >> * PairwiseSequenceAlignerType.LOCAL, new >> SimpleGapPenalty(), matrix);* >> *for (SequencePair<ProteinSequence, AminoAcidCompound> pair : alig) {* >> * System.out.printf("%n%s vs %s%n%s", >> pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);* >> *}* >> It is told me to create these two classes. >> >> I am using the last version of the BioJava project (4.2.1) by means of >> Maven (as described in the site). >> Probably in that version there are not anymore those classes*. *Could be >> this the problem? >> How could I solve this? >> >> Thanks a lot. >> >> P.S. >> Regarding the "BioJavaTutorial page - book 2: The Alignment module" ( >> https://github.com/biojava/biojava-tutorial/blob/master/alignment/README.md), >> could be possible kindly to have the explanation of the pages? >> Unfortunaltely it is the onyl part of the tutorial without explanation. >> >> >> 2016-05-24 14:12 GMT+02:00 Andrea Battistelli <[email protected]>: >> >>> Hi Andreas. >>> >>> Thank you very much for the fixes. Surely it will help me. >>> I have understood the problem you encountered with the old site. >>> Now I will try to apply those things. >>> >>> Thanks again, >>> Andrea >>> >>> 2016-05-23 19:27 GMT+02:00 Andreas Prlic <[email protected]>: >>> >>>> Hi Andrea, >>>> >>>> Sorry for the inconvenience. We had to turn the old site off, since >>>> there were too many security breaches which resulted in content spamming. >>>> This is across all bio* projects... >>>> >>>> I fixed the links on the CookBook4 page. Checking some of the related >>>> pages, there are still a lot of formatting issues. That will take a bit to >>>> fix them all up. However, each page at the bottom has an "edit this page" >>>> link, which makes it easy to access the raw markdown content. It is >>>> possible to see the code in a more readable way. I also fixed up this page >>>> for now: http://biojava.org/wikis/BioJava:CookBook3:PSA/ >>>> >>>> Hope that helps, >>>> >>>> Andreas >>>> >>>> >>>> >>>> On Sat, May 21, 2016 at 4:09 AM, Andrea Battistelli < >>>> [email protected]> wrote: >>>> >>>>> Hello everyone. >>>>> >>>>> I have been studying the pairwise sequence alignment concept for a >>>>> project that I need to do for an exam. >>>>> In particular I am interested in the global and local alignments and >>>>> all the things related to them (how they are implemented, how I can >>>>> generate a paiwise alignment, ect.). >>>>> I would implement my project in Java employing indeed BioJava as >>>>> starting point. >>>>> I set up correctly the Maven project on Eclipse so no problem under >>>>> that point of view. >>>>> >>>>> Few months ago I have seen there was all the documentation, tutorials >>>>> and specifications about the BioJava project based on the Wiki pages. >>>>> I have seen it has been all migrated into a new web site but now I am >>>>> not finding any documentation, tutorial or cookbook about the topic of >>>>> personal interest. >>>>> >>>>> - In the BioJavaTutorial page - book 2, the alignment module has no >>>>> pages of explanation. >>>>> - In the CookBook4.0, all the links relative to the paiwise sequence >>>>> alignment give me back an "address uninterpretable" message. >>>>> - Finally in the Wiki Pages section there are many links. In some of >>>>> these there are links interesting for me but they contain not well >>>>> formatted codes. >>>>> >>>>> I know that it may taketime to migrate all the things but in the >>>>> meantime: >>>>> Is there any possibility to have the reference to the old web site? >>>>> Anyone can help me to indicate me where I can find some good pages of >>>>> documentation, tutorial, etc. about pairwise sequence alignment for BioJava? >>>>> >>>>> Thanks a lot. >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> ----------------------------------------------------------------------- >>>> >>> >>> >> > > > > --001a113b18e8cfdc5c0533a86e86 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div><div>Ok understood, sorry.<br></div>Now it works, tha= nk you Andreas.<br></div></div><div class=3D"gmail_extra"><br><div class=3D= "gmail_quote">2016-05-24 20:30 GMT+02:00 Andreas Prlic <span dir=3D"ltr">&l= t;<a href=3D"mailto:[email protected]" target=3D"_blank">[email protected]</a= >></span>:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8= ex;border-left:1px #ccc solid;padding-left:1ex"><div dir=3D"ltr">Hi Andreas= ,<div><br></div><div>please don't mail me directly with questions, but = keep them on the list, for the benefit of other users who might be in the s= ame situation.</div><div><br></div><div>You are right, the signature of Sub= stitutionMatrix has changed at some point in the past. Try this:</div><div>= <br></div><div><pre style=3D"color:rgb(0,0,0);font-family:Menlo;font-size:9= pt">SubstitutionMatrix<AminoAcidCompound> matrix =3D SubstitutionMatr= ixHelper.<span style=3D"font-style:italic">getBlosum65</span>();</pre><pre>= <font face=3D"arial, helvetica, sans-serif"><br></font></pre><pre><font fac= e=3D"arial, helvetica, sans-serif">There is also another example in the &qu= ot;demo" package of the alignment module, that you could take a look a= t.<br><br>About the tutorial: When you have the basics figured out, any con= tributions/pull requests to improve the tutorial will be welcome! ;-)</font= ><span class=3D"HOEnZb"><font color=3D"#888888"><br><br>A</font></span></pr= e><pre style=3D"color:rgb(0,0,0);font-family:Menlo;font-size:9pt"><br></pre= ><pre style=3D"color:rgb(0,0,0);font-family:Menlo;font-size:9pt"><br></pre>= </div><div><div class=3D"h5"><div class=3D"gmail_extra"><br><div class=3D"g= mail_quote">On Tue, May 24, 2016 at 5:51 AM, Andrea Battistelli <span dir= =3D"ltr"><<a href=3D"mailto:[email protected]" target=3D"_blank">a= [email protected]</a>></span> wrote:<br><blockquote class=3D"gmail_= quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1= ex"><div dir=3D"ltr"><div><div>Hi Andreas.<br><br></div>I have seen the cod= es in the page you suggested me.<br>I have encountered some errors about:<b= r><br><div style=3D"margin-left:40px"><i>import org.biojava.nbio.alignment.= template.SequencePair;</i><br></div><div style=3D"margin-left:40px"><i>impo= rt org.biojava.nbio.alignment.template.SubstitutionMatrix;<br><br></i></div= ></div><div>Regarding all the other imports, there are not problems.<br></d= iv><div>Indeed in the code I have errors in this part:<br><br><div style=3D= "margin-left:40px"><i><b><u>SubstitutionMatrix</u></b><AminoAcidCompound= > matrix =3D new SimpleSubstitutionMatrix<AminoAcidCompound>();</i= ><br></div><div style=3D"margin-left:40px"><i>List<<b><u>SequencePair</u= ></b><ProteinSequence, AminoAcidCompound>> alig =3D Alignments.get= AllPairsAlignments(lst,</i><br></div><div style=3D"margin-left:40px"><i>=C2= =A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 Pa= irwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), matrix);</i><br></= div><div style=3D"margin-left:40px"><i>for (<b><u>SequencePair</u></b><P= roteinSequence, AminoAcidCompound> pair : alig) {</i><br></div><div styl= e=3D"margin-left:40px"><i>=C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0=C2= =A0=C2=A0 System.out.printf("%n%s vs %s%n%s", pair.getQuery().get= Accession(), pair.getTarget().getAccession(), pair);</i><br></div><div styl= e=3D"margin-left:40px"><i>}</i><br></div></div><div>It is told me to create= these two classes.<br><br></div><div>I am using the last version of the Bi= oJava project (4.2.1) by means of Maven (as described in the site).<br>Prob= ably in that version there are not anymore those classes<i>. </i>Could be t= his the problem?<br></div><div>How could I solve this?<br><br></div><div>Th= anks a lot.<br></div><div><br></div><div>P.S. <br>Regarding the "BioJa= vaTutorial page - book 2: The Alignment module" (<a href=3D"https://gi= thub.com/biojava/biojava-tutorial/blob/master/alignment/README.md" target= =3D"_blank">https://github.com/biojava/biojava-tutorial/blob/master/alignme= nt/README.md</a>), could be possible kindly to have the explanation of the = pages?<br></div><div>Unfortunaltely it is the onyl part of the tutorial wit= hout explanation.<br></div><div><i><br></i></div></div><div><div><div class= =3D"gmail_extra"><br><div class=3D"gmail_quote">2016-05-24 14:12 GMT+02:00 = Andrea Battistelli <span dir=3D"ltr"><<a href=3D"mailto:andreyas.1688@gm= ail.com" target=3D"_blank">[email protected]</a>></span>:<br><bloc= kquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #cc= c solid;padding-left:1ex"><div dir=3D"ltr"><div><div><div><div>Hi Andreas.<= br><br></div>Thank you very much for the fixes. Surely it will help me.<br>= </div>I have understood the problem you encountered with the old site.<br><= /div>Now I will try to apply those things.<br><br></div><div>Thanks again,<= br></div><div>Andrea<br></div></div><div><div><div class=3D"gmail_extra"><b= r><div class=3D"gmail_quote">2016-05-23 19:27 GMT+02:00 Andreas Prlic <span= dir=3D"ltr"><<a href=3D"mailto:[email protected]" target=3D"_blank">andr= [email protected]</a>></span>:<br><blockquote class=3D"gmail_quote" style=3D"= margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir=3D"= ltr">Hi Andrea,<div><br></div><div>Sorry for the inconvenience. We had to t= urn the old site off, since there were too many security breaches which res= ulted in content spamming. This is across all bio* projects...</div><div><b= r></div><div>I fixed the links on the CookBook4 page. Checking some of the = related pages, there are still a lot of formatting issues. That will take a= bit to fix them all up. However, each page at the bottom has an "edit= this page" link, which makes it easy to access the raw markdown conte= nt.=C2=A0 It is possible to see the code in a more readable way. I also fix= ed up this page for now: <a href=3D"http://biojava.org/wikis/BioJava:CookBo= ok3:PSA/" target=3D"_blank">http://biojava.org/wikis/BioJava:CookBook3:PSA/= </a></div><div><br></div><div>Hope that helps,</div><div><br></div><div>And= reas<br><div><br></div></div><div><br></div></div><div class=3D"gmail_extra= "><br><div class=3D"gmail_quote"><div><div>On Sat, May 21, 2016 at 4:09 AM,= Andrea Battistelli <span dir=3D"ltr"><<a href=3D"mailto:andreyas.1688@g= mail.com" target=3D"_blank">[email protected]</a>></span> wrote:<b= r></div></div><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;= border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir=3D"ltr"><di= v><div><div><div><div><div>Hello everyone.<br><br></div>I have been studyin= g the pairwise sequence alignment concept for a project that I need to do f= or an exam.<br></div><div>In particular I am interested in the global and l= ocal alignments and all the things related to them (how they are implemente= d, how I can generate a paiwise alignment, ect.).<br></div>I would implemen= t my project in Java employing indeed BioJava as starting point.<br></div><= div>I set up correctly the Maven project on Eclipse so no problem under tha= t point of view.<br></div><div><br></div>Few months ago I have seen there w= as all the documentation, tutorials and specifications about the BioJava pr= oject based on the Wiki pages.<br></div>I have seen it has been all migrate= d into a new web site but now I am not finding any documentation, tutorial = or cookbook about the topic of personal interest.<br><br></div>- In the Bio= JavaTutorial page - book 2, the alignment module has no pages of explanatio= n.<br></div><div>- In the CookBook4.0, all the links relative to the paiwis= e sequence alignment give me back an "<span lang=3D"en"><span>address<= /span> <span>uninterpretable</span></span>" message.<br></div><div>- F= inally in the Wiki Pages section there are many links. In some of these the= re are links interesting for me but they contain not well formatted codes.<= br><br></div><div>I know that it may taketime to migrate all the things but= in the meantime:<br>Is there any possibility to have the reference to the = old web site?<br></div><div>Anyone can help me to indicate me where I can f= ind some good pages of documentation, tutorial, etc. about pairwise sequenc= e alignment for BioJava?<br><br></div><div>Thanks a lot.<br></div></div> <br></div></div>_______________________________________________<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" rel=3D"n= oreferrer" target=3D"_blank">http://mailman.open-bio.org/mailman/listinfo/b= iojava-l</a><span><font color=3D"#888888"><br></font></span></blockquote></= div><span><font color=3D"#888888"><br><br clear=3D"all"><div><br></div>-- <= br><div><div dir=3D"ltr"><div><div dir=3D"ltr">----------------------------= -------------------------------------------<br>Dr. Andreas Prlic<br>RCSB PD= B Protein Data Bank</div><div>Technical & Scientific Team Lead</div><di= v dir=3D"ltr">University of California, San Diego<div><br></div><div>Editor= Software Section=C2=A0<br><div>PLOS Computational Biology<div><div><div><b= r></div><div>BioJava Project Lead<br>--------------------------------------= ---------------------------------<br></div></div></div></div></div></div></= div></div></div> </font></span></div> </blockquote></div><br></div> </div></div></blockquote></div><br></div> </div></div></blockquote></div><br><br clear=3D"all"><div><br></div><div><d= iv dir=3D"ltr"><div><div dir=3D"ltr"><div><div><div><div><div><br></div></d= iv></div></div></div></div></div></div></div> </div></div></div></div> </blockquote></div><br></div> --001a113b18e8cfdc5c0533a86e86-- --===============8806665391984828344== 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 --===============8806665391984828344==--