Hi TT A couple of issues with the GFF file that I can spot that will not be liked by Artemis . There are some STS features with no ID tag and some gene features with non-unique ID¹s (e.g. ID=ACBP).
You can directly load in the GenBank file without converting it, which is probably preferable. Regards Tim On 4/4/11 9:46 PM, "Tony Tang" <ttony...@gmail.com> wrote: > Hello All, > I have a question of reading certain gff3 file using Artemis 13. While I was > trying to open the file, I received the following error message: > > Exception in thread "Thread-2" java.lang.NullPointerException > at > uk.ac.sanger.artemis.io.GFFDocumentEntry.combineGeneFeatures(GFFDocumentEntry. > java:224) > at > uk.ac.sanger.artemis.io.GFFDocumentEntry.<init>(GFFDocumentEntry.java:76) > at > uk.ac.sanger.artemis.io.DocumentEntryFactory.makeDocumentEntry(DocumentEntryFa > ctory.java:122) > at > uk.ac.sanger.artemis.components.EntryFileDialog.getEntryFromFileHelper(EntryFi > leDialog.java:240) > at > uk.ac.sanger.artemis.components.EntryFileDialog.getEntryFromFile(EntryFileDial > og.java:300) > at > uk.ac.sanger.artemis.components.EntryFileDialog.getEntry(EntryFileDialog.java: > 212) > at > uk.ac.sanger.artemis.components.FileDialogEntrySource.getEntryInternal(FileDia > logEntrySource.java:231) > at > uk.ac.sanger.artemis.components.FileDialogEntrySource.getEntry(FileDialogEntry > Source.java:105) > at > uk.ac.sanger.artemis.components.ArtemisMain$8.construct(ArtemisMain.java:713) > at > uk.ac.sanger.artemis.components.SwingWorker$2.run(SwingWorker.java:127) > at java.lang.Thread.run(Thread.java:636) > The gff3 file was converted from gbk file which can be found here > (ftp://ftp.bio.net/biomirror/ncbigenomes/Protozoa/Plasmodium_falciparum/NC_004 > 314.gbk.gz > ) by bp_genbank2gff3.pl <http://bp_genbank2gff3.pl> . > > Anyone has encounter the same problem before? > > Thanks, > TT > > > _______________________________________________ > Artemis-users mailing list > Artemis-users@sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
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