[Biojava-l] A bug in Class "org.biojavax.bio.seq.io.GenbankFormat"

[Huijie Qiao]

version 1.7.1

line 361
else if (sectionKey.equals(SOURCE_TAG)) {
      // ignore - can get all this from the first feature

actually the content in the SOURCE_TAG and the first feature are different
in some gb file.

For example, the example file in
http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchseq_help.html
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5&rettype=gb

The Source TAG is
SOURCE      Bos taurus (cattle)
  ORGANISM  Bos taurus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
Euteleostomi;
            Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Ruminantia;
            Pecora; Bovidae; Bovinae; Bos.

and the first feature tag is
FEATURES             Location/Qualifiers
     source          1..1136
                     /organism="Bos taurus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9913"
                     /clone="pBB2I"
                     /tissue_type="liver"

I can't get the hierarchy info through the follow codes.
NCBITaxon taxon = seq.getTaxon();
System.out.println(taxon.getNameHierarchy()); output is "."