<div dir="ltr"><div><div>Dear Andreas,<br>Thank you for your answer. The file I'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">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000009065.1_ASM906v1/GCA_000009065.1_ASM906v1_genomic.gbff.gz</a><br><br>I'm trying to access information stored in CDS tags. The code I'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<String, ChromosomeSequence> ss = gbProxyReader.process();<br><br> for (DNASequence s : ss.values()) {<br> List<FeatureInterface<AbstractSequence<NucleotideCompound>, NucleotideCompound>> 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'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="gmail_extra"><br><div class="gmail_quote">2014-09-22 18:28 GMT+02:00 Andreas Prlic <span dir="ltr"><<a href="mailto:andreas@sdsc.edu" target="_blank">andreas@sdsc.edu</a>></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'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 class="h5">On Mon, Sep 15, 2014 at 11:20 AM, Paolo Pavan <span dir="ltr"><<a href="mailto:paolo.pavan@gmail.com" target="_blank">paolo.pavan@gmail.com</a>></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 class="h5"><div dir="ltr"><div><div>Dear all,<br></div>I'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=="FEATURES") 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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