<div dir="ltr"><div class="gmail_default" style="font-family:tahoma,sans-serif">Sure,</div><div class="gmail_default" style="font-family:tahoma,sans-serif"><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif">I'm up for that. I'm just trying to look at the code on GitHub to try and get a feel for the project. Then I might be able to better contribute</div><div class="gmail_default" style="font-family:tahoma,sans-serif"><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif">Simon</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jun 4, 2015 at 2:49 PM, Andreas Prlic <span dir="ltr"><<a href="mailto:andreas@sdsc.edu" target="_blank">andreas@sdsc.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Paolo and Simon,<div><br></div><div>Would it be possible to update the documentation in the tutorial, so other users can see how to retrieve features as well? Also, perhaps file a ticket for the missing keywords, etc. fields , so this does not get lost?</div><div><br></div><div><a href="https://github.com/biojava/biojava-tutorial/blob/master/genomics/genebank.md" target="_blank">https://github.com/biojava/biojava-tutorial/blob/master/genomics/genebank.md</a><br></div><div><br></div><div>Thanks!</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>Andreas</div></font></span><div><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jun 4, 2015 at 2:57 AM, simon rayner <span dir="ltr"><<a href="mailto:simon.rayner.cn@gmail.com" target="_blank">simon.rayner.cn@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div style="font-family:tahoma,sans-serif">We resolved things, sort of, But at some point we fell off the mailing list. Here is the full message chain</div><div style="font-family:tahoma,sans-serif"><br></div><div style="font-family:tahoma,sans-serif">thanks again to all for the help</div><div style="font-family:tahoma,sans-serif"><br></div><div style="font-family:tahoma,sans-serif">Andreas, repeating my question here, would it be any use if I added a more complete code sample to the tutorial show how to pull the Feature information out of a GenBank file?</div><div style="font-family:tahoma,sans-serif"><br></div><div style="font-family:tahoma,sans-serif">cheers</div><div style="font-family:tahoma,sans-serif"><br></div><div style="font-family:tahoma,sans-serif">Simon</div><div style="font-family:tahoma,sans-serif"><br></div><div style="font-family:tahoma,sans-serif"><br></div><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Paolo Pavan</b> <span dir="ltr"><<a href="mailto:paolo.pavan@gmail.com" target="_blank">paolo.pavan@gmail.com</a>></span><br>Date: Wed, Jun 3, 2015 at 5:34 PM<br>Subject: Re: [Biojava-l] GenBank parsing<br>To: simon rayner <<a href="mailto:simon.rayner.cn@gmail.com" target="_blank">simon.rayner.cn@gmail.com</a>><br><br><br><div dir="ltr"><div><div>Oh, I'm realizing now that we went outside of the mailing list.<br></div>You can forward all the conversation to the list and ask for Andreas there.<span><font color="#888888"><br><br></font></span></div><span><font color="#888888">Paolo<br></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">2015-06-03 17:29 GMT+02:00 Paolo Pavan <span dir="ltr"><<a href="mailto:paolo.pavan@gmail.com" target="_blank">paolo.pavan@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><div>Simon,<br></div>As far as I have read on the mailing list, I know that Andreas Prlic is interested in this kind of collaborations. I think he will answer you shortly.<br><br></div>Bye bye!<br></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">2015-06-03 17:14 GMT+02:00 simon rayner <span dir="ltr"><<a href="mailto:simon.rayner.cn@gmail.com" target="_blank">simon.rayner.cn@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div style="font-family:tahoma,sans-serif">Hi Paolo</div><div style="font-family:tahoma,sans-serif"><br></div><div style="font-family:tahoma,sans-serif">I think its okay. For now, perhaps it would be good to clarify this somewhere (perhaps in the tutorial sample?). And would it be any use if I added a more complete code sample to the tutorial show how to pull the Feature information out of a GenBank file?</div><span><font color="#888888"><div style="font-family:tahoma,sans-serif"><br>Simon</div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote"><span>On Wed, Jun 3, 2015 at 5:11 PM, Paolo Pavan <span dir="ltr"><<a href="mailto:paolo.pavan@gmail.com" target="_blank">paolo.pavan@gmail.com</a>></span> wrote:<br></span><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Hi Simon,<br></div>Now I see what you mean and unfortunately I must say that those retrieval are not supported yet. They aren't in the section I put my hands on and I must say that I wasn't actually aware of that.<br><br></div>The file responsible for this behaviour is GenbankSequenceParser.java, I don't know if there are someone of the original authors out of there that can add something.<br></div><div><br>You are unlucky, let me know if I can be of any help more.<span><font color="#888888"><br></font></span></div></div><span><font color="#888888">Paolo<br></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">2015-06-03 15:55 GMT+02:00 simon rayner <span dir="ltr"><<a href="mailto:simon.rayner.cn@gmail.com" target="_blank">simon.rayner.cn@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div style="font-family:tahoma,sans-serif">Hi Paolo</div><div style="font-family:tahoma,sans-serif"><br></div><div style="font-family:tahoma,sans-serif"><span style="font-family:arial,sans-serif;font-size:12.8000001907349px"> sequence.getFeaturesByType("</span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">source");</span></div><div style="font-family:tahoma,sans-serif"><span style="font-family:arial,sans-serif;font-size:12.8000001907349px"><br></span></div><div style="font-family:tahoma,sans-serif"><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">will return the 'source' entry at the top of the FEATURE tree, but it won't help me retrieve anything outside the FEATURE tree (from the top of the file and at the bottom before the sequence)</span></div><div style="font-family:tahoma,sans-serif"><span style="font-family:arial,sans-serif;font-size:12.8000001907349px"><br></span></div><div style="font-family:tahoma,sans-serif"><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">For example, in the following GenBank file</span></div><div style="font-family:tahoma,sans-serif"><span style="font-family:arial,sans-serif;font-size:12.8000001907349px"><br></span></div><div style="font-family:tahoma,sans-serif"><pre style="font-family:monospace,serif;font-size:13px;white-space:pre-wrap;margin-top:0px;margin-bottom:0px;overflow:visible;word-wrap:break-word;width:50em;zoom:1;color:rgb(0,0,0);line-height:16.8999996185303px">LOCUS AY102993 400 bp mRNA linear VRL 22-FEB-2006
DEFINITION Rabies virus isolate RV61 nucleoprotein mRNA, partial cds.
ACCESSION AY102993 AY247649
VERSION AY102993.2 GI:34099643
KEYWORDS .
SOURCE Rabies virus
ORGANISM <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=11292" style="color:rgb(100,42,143)" target="_blank">Rabies virus</a>
Viruses; ssRNA viruses; ssRNA negative-strand viruses;
Mononegavirales; Rhabdoviridae; Lyssavirus.
REFERENCE 1 (bases 1 to 400)
AUTHORS Smith,J., McElhinney,L., Parsons,G., Brink,N., Doherty,T.,
Agranoff,D., Miranda,M.E. and Fooks,A.R.
TITLE Case report: rapid ante-mortem diagnosis of a human case of rabies
imported into the UK from the Philippines
JOURNAL J. Med. Virol. 69 (1), 150-155 (2003)
PUBMED <a href="http://www.ncbi.nlm.nih.gov/pubmed/12436491" style="color:rgb(100,42,143)" target="_blank">12436491</a>
REFERENCE 2 (bases 1 to 400)
</pre><div><div> .</div></div><div><div> .</div></div><div><div> .</div></div><div><br></div><div><pre style="font-family:monospace,serif;font-size:13px;white-space:pre-wrap;margin-top:0px;margin-bottom:0px;overflow:visible;word-wrap:break-word;width:50em;zoom:1;color:rgb(0,0,0);line-height:16.8999996185303px">COMMENT On Aug 22, 2003 this sequence version replaced gi:<a href="http://www.ncbi.nlm.nih.gov/nuccore/25986720" style="color:rgb(100,42,143)" target="_blank">25986720</a>.
<a name="14dbe9ec826f05c2_14dbd665e8866ce9_14dba0fa58af8a34_14dba0abfda2cc98_14db9fcde85d2381_14db9fa16f3d17e9_14db9b4ac1135cbb_feature_34099643" style="color:rgb(47,74,139)"></a>FEATURES Location/Qualifiers
<span> source 1..400
/organism="Rabies virus"
/mol_type="mRNA"
/isolate="RV61"
/host="Homo sapiens"
/db_xref="taxon:<a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=11292" style="color:rgb(100,42,143)" target="_blank">11292</a>"
/country="United Kingdom"
/note="isolated in 1987"
</span><span> <a href="http://www.ncbi.nlm.nih.gov/nuccore/34099643?from=1&to=400&sat=4&sat_key=38832925" style="text-decoration:none;border-bottom-width:1px;border-bottom-style:dotted;border-bottom-color:blue;color:rgb(100,42,143)" target="_blank">CDS</a> 1..>400
</span></pre></div><div><br></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">sequence.getFeaturesByType("</span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">source");</span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px"><br></span></span></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px"><br></span></span></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">will return the portion</span></span></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px"><br></span></span></div><pre style="font-size:13px;font-family:monospace,serif;white-space:pre-wrap;margin-top:0px;margin-bottom:0px;overflow:visible;word-wrap:break-word;width:50em;zoom:1;color:rgb(0,0,0);line-height:16.8999996185303px"><span> source 1..400
/organism="Rabies virus"
/mol_type="mRNA"
/isolate="RV61"
/host="Homo sapiens"
/db_xref="taxon:<a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=11292" style="color:rgb(100,42,143)" target="_blank">11292</a>"
/country="United Kingdom"
/note="isolated in 1987"
</span></pre><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px"><br></span></span></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px"><br></span></span></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">which is important data, but what about the KEYWORDS, SOURCE and REFERENCE information at the top and COMMENT at the bottom?</span></span></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px"><br></span></span></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">I can use the following calls to get some information</span></span></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px"><br></span></span></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">getOriginalHeader() -> LOCUS</span></span></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">getDescription() -> DEFINITION</span></span></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">getAccession() -> ACCESSION </span></span></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px"><br></span></span></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">What am I missing here?</span></span></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px"><br></span></span></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">thanks</span></span></div><span><font color="#888888"><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px"><br></span></span></div><div><span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">Simon</span></span></div></font></span></div></div><div><div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jun 3, 2015 at 3:22 PM, Paolo Pavan <span dir="ltr"><<a href="mailto:paolo.pavan@gmail.com" target="_blank">paolo.pavan@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Can't you find those information in the "source" feature? Check this list: </div>List l = sequence.getFeaturesByType("source");<br><br></div>This come from the fact that in new version of genbank file, source is a compulsory feature and they move many info from top level "Features tag" into "Source" tag qualifiers.<br><br></div>Let us know,<br></div>Paolo<br><div><div><br></div></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">2015-06-03 14:29 GMT+02:00 simon rayner <span dir="ltr"><<a href="mailto:simon.rayner.cn@gmail.com" target="_blank">simon.rayner.cn@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div style="font-family:tahoma,sans-serif">Thanks to all for taking the time to answer. </div><div style="font-family:tahoma,sans-serif"><br></div><div style="font-family:tahoma,sans-serif">I had already got as far as parsing out the feature information using something like</div><div style="font-family:tahoma,sans-serif"><br></div><div style="font-family:tahoma,sans-serif"><div><span style="white-space:pre-wrap"> </span>LinkedHashMap<String, DNASequence> dnaSequences = GenbankReaderHelper.readGenbankDNASequence( dnaFile );</div><div><span style="white-space:pre-wrap"> </span>for (DNASequence sequence : dnaSequences.values()) {</div><div><br></div></div><div><div style="font-family:tahoma,sans-serif"> List<FeatureInterface<AbstractSequence<NucleotideCompound>, NucleotideCompound>> fl = sequence.getFeatures();</div><div style="font-family:tahoma,sans-serif"> for (FeatureInterface fi : fl) {</div><div style="font-family:tahoma,sans-serif"><br></div><div><div><font face="tahoma, sans-serif"> HashMap <String, Qualifier> quals = fi.getQualifiers();</font></div><div><font face="tahoma, sans-serif"> for(Map.Entry<String, Qualifier> entry : quals.entrySet()){</font></div><div><font face="tahoma, sans-serif"> <a href="http://logger.info" target="_blank">logger.info</a>("--\t" + entry.getKey() + "\t|\t" + entry.getValue().getName() </font></div><div><font face="tahoma, sans-serif"> + " / " + entry.getValue().getValue() + "\\" + entry.getValue().toString()); </font></div><div><font face="tahoma, sans-serif"> }</font></div></div><div><div style="font-family:tahoma,sans-serif"> <a href="http://logger.info" target="_blank">logger.info</a>("SHORT\t" + fi.getShortDescription());</div><div style="font-family:tahoma,sans-serif"> <a href="http://logger.info" target="_blank">logger.info</a>("SOURCE\t" + fi.getSource());</div><div style="font-family:tahoma,sans-serif"> <a href="http://logger.info" target="_blank">logger.info</a>("TYPE\t" + fi.getType());</div><div style="font-family:tahoma,sans-serif"> <a href="http://logger.info" target="_blank">logger.info</a>("HASHCODE\t" + fi.hashCode());</div><div style="font-family:tahoma,sans-serif"> <a href="http://logger.info" target="_blank">logger.info</a>("-");</div><div style="font-family:tahoma,sans-serif"> }</div><div style="font-family:tahoma,sans-serif"><br></div><div><div><font face="tahoma, sans-serif"><span style="white-space:pre-wrap"> </span>}</font></div></div><div style="font-family:tahoma,sans-serif"><br></div><div style="font-family:tahoma,sans-serif">But I am still stumped as to how to access the annotation information at the top of a GenBank file. </div><div style="font-family:tahoma,sans-serif"><br></div><div style="font-family:tahoma,sans-serif">For example, getAccession gets me the accession number of the sequence, but what about all the other data that is there (e.g. the pubmed records)?</div><div style="font-family:tahoma,sans-serif"><br></div><div style="font-family:tahoma,sans-serif">In BJ3, there was a RichAnnotation class, but I don't see anything equivalent in BJ4.</div><div style="font-family:tahoma,sans-serif"><br></div><div style="font-family:tahoma,sans-serif">cheers</div><span><font color="#888888"><div style="font-family:tahoma,sans-serif"><br></div><div style="font-family:tahoma,sans-serif">Simon</div><div style="font-family:tahoma,sans-serif"><br></div><div style="font-family:tahoma,sans-serif"><br></div></font></span></div></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jun 3, 2015 at 12:39 PM, Paolo Pavan <span dir="ltr"><<a href="mailto:paolo.pavan@gmail.com" target="_blank">paolo.pavan@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><div><div>Hi Simon, <br></div>I took care about last updates to the Genbank parser (reader). At the state of the art, there are two ways to read annotated Genbank files: <span lang="EN-US">via </span><span lang="EN-US"><span lang="EN-US">GenbankReader </span>and via </span><span lang="EN-US"><span lang="EN-US"><span lang="EN-US"></span>GenbankProxySequenceReader </span>. <br><br></span></div><span lang="EN-US">The first one:<br>GenbankReader<ProteinSequence, AminoAcidCompound> GenbankProtein<br> = new GenbankReader<ProteinSequence, AminoAcidCompound>(<br> inStream,<br> new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),<br> new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())<br> );<br>LinkedHashMap<String, ProteinSequence> proteinSequences = GenbankProtein.process();<br> inStream.close();<br><br></span><br><span lang="EN-US"><span lang="EN-US">The second one is:<br><br></span>GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader<br> = new GenbankProxySequenceReader<AminoAcidCompound>("/my_directory", "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());<br> ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);<br><br><br></span></div><div><span lang="EN-US">Just keep in mind to use NucleotideCompound and a DNASequenceCreator(DNACompoundSet.getDNACompoundSet()) if you need to parse genbank nucleotide files.<br><br></span></div><div><span lang="EN-US">You can access annotation stored via getFeatures() methods family of the readed sequence object. Also note that features have qualifiers (those starting with / in the genbank file) and they must be accessed from the feature object with getQualifiers(). <br>Also note that feature can have complex locations (rare, but present) in this case you will find nested locations in the feature retrieved.<br><br></span></div><div><span lang="EN-US">Does this answer your question?<br></span></div><div><span lang="EN-US">Bye bye,<br>Paolo<br></span></div><div><span lang="EN-US"><br></span></div><div><span lang="EN-US"><br><br></span></div><span lang="EN-US"><br></span><div><div><span lang="EN-US"><br></span></div></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">2015-06-03 10:27 GMT+02:00 Jose Manuel Duarte <span dir="ltr"><<a href="mailto:jose.duarte@psi.ch" target="_blank">jose.duarte@psi.ch</a>></span>:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">I can't offer much help regarding GenBank parsing itself, but I would at least like to clarify the situation with the different (indeed confusing) versions:<br>
<br>
BJ4 is the current release, well maintained and under development. BJ3 has been completely superseded by BJ4. That means that BJ4 does everything that BJ3 did. In the cookbook and tutorials everything that refers to BJ3 should work in BJ4, with the only difference that the namespace of packages has changed from org.biojava.bio/org.biojava3 to org.biojava.nbio.<br>
<br>
BJ1 and BJX are both legacy projects, with some maintenance but not much active development. I believe that some of the features in them were not ported to BJ3+.<br>
<br>
Cheers<span><font color="#888888"><br>
<br>
Jose</font></span><div><div><br>
<br>
<br>
On <a href="tel:02.06.2015%2011" value="+390206201511" target="_blank">02.06.2015 11</a>:40, Simon Rayner wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Hi<br>
<br>
I'm coming back to BioJava (BJ) after a couple of years away and am somewhat confused by the current collection of cookbooks, tutorials and APIs. There appear to be a few examples for handling protein structure data, but relatively little for more mainstream stuff such as parsing Genbank files, which I first need to get the information I want to investigate protein structure. But when I look at the relevant code samples to do this, they refer back to BJ3, BJ1, or even BJX. Even the Wiki page still refers to BJ3 despite the release of BJ4 back in Feb 2015.<br>
<br>
I have everything working for parsing GenBank data, but I'm still trying to get the Annotation information out of the top of a GenBank file, and can't find any way of doing this using BJ4 - the BJ4 API appears to refer to the RichAnnotation type in BJX release. Can anyone clarify what you are supposed to do here? Start mixing in some BJX? (and is BJX still active?) or should I still be using BJ3 until BJ4 stabilizes. I realise this is an open source project, but some clarification on the current status of things would be handy if the project is going to appeal to a larger community :)<br>
<br>
Thanks!<br>
<br>
<br>
<br>
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