<div dir="ltr"><div><div>Dear Andreas,<br></div>I have gone deep in it. I had a look inside the code and I&#39;ve modified it to accomplish the task. If you find it appropriate I can contribute with it.<br><br></div>Cheers,<br>Paolo<br><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2014-09-24 0:12 GMT+02:00 Paolo Pavan <span dir="ltr">&lt;<a href="mailto:paolo.pavan@gmail.com" target="_blank">paolo.pavan@gmail.com</a>&gt;</span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Dear Andreas,<br>Thank you for your answer. The file I&#39;m trying to load has been downloaded from the link below:<br><a href="ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000009065.1_ASM906v1/GCA_000009065.1_ASM906v1_genomic.gbff.gz" target="_blank">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000009065.1_ASM906v1/GCA_000009065.1_ASM906v1_genomic.gbff.gz</a><br><br>I&#39;m trying to access information stored in CDS tags. The code I&#39;m using to parse is:<br><br>        org.biojava3.core.sequence.compound.DNACompoundSet compoundSet<br>                = new AmbiguityDNACompoundSet();<br>        org.biojava3.core.sequence.io.template.SequenceParserInterface parser<br>                = new GenbankSequenceParser();<br><br>        for (String fn : fileNames) {<br>            File f = new File(fn);<br>            GenbankReader gbProxyReader<br>                    = new GenbankReader(<br>                            f,<br>                            new GenericGenbankHeaderParser(),<br>                            new FileProxyDNASequenceCreator(<br>                                    f,<br>                                    compoundSet,<br>                                    parser<br>                            )<br>                    );<br>            LinkedHashMap&lt;String, ChromosomeSequence&gt; ss = gbProxyReader.process();<br><br>            for (DNASequence s : ss.values()) {<br>                List&lt;FeatureInterface&lt;AbstractSequence&lt;NucleotideCompound&gt;, NucleotideCompound&gt;&gt; features = s.getFeatures();<br>                <br>                System.out.println(features.size());<br>    }<br><br></div>I have had a look at the code and maybe it could be that I&#39;m missing something. For instance, am I using the right DNASequenceCreator / FileProxyDNASequenceCreator? <br></div><div><br></div>Thank you,<br>Paolo<br><div><br><br></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">2014-09-22 18:28 GMT+02:00 Andreas Prlic <span dir="ltr">&lt;<a href="mailto:andreas@sdsc.edu" target="_blank">andreas@sdsc.edu</a>&gt;</span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>apologies for the slow response.  Can you point us to the file that you can&#39;t parse so we can take a look?</div><div><br></div><div>Andreas</div><div><br></div><div><br><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Mon, Sep 15, 2014 at 11:20 AM, Paolo Pavan <span dir="ltr">&lt;<a href="mailto:paolo.pavan@gmail.com" target="_blank">paolo.pavan@gmail.com</a>&gt;</span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><div><div>Dear all,<br></div>I&#39;m having trouble in parsing a genbank flat file file using GenbankReader. While the sequence and some global information are loaded correctly, I cannot load annotations (i.e. those in sectionKey==&quot;FEATURES&quot;) and s.getFeatures().size() == 0 .<br>Am I missing something? Before posting the code, is the GenbankReader in biojava3.1.0 a still in progress parser?<br><br></div>Thank you,<br>Paolo<br></div>
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