[Biojava-l] Genbank file parser error

[Mark Schreiber]

I assume that the downloaded file has the complete sequence in it? Probably
worth checking that it has the complete sequence block (all 116366104 bp).

- Mark

On Thu, Jan 29, 2009 at 12:51 PM, gang wu <gwu at molbio.mgh.harvard.edu>wrote:

> Hi Everyone,
>
> I have a piece of code to parse Genbank file and retrieve gene sequence and
> related information. It works well with sequences such as Arabidopsis
> thaliana, C. elegans, Bos taurus. But it failed with Mus musculus chromosome
> 2. The contig that the code failed on is the largest one in my test. Contig
> NT_039207 has 116366104 bp, but the code shows it's cut to 100000020 bp.
> That causes some gene coordinates out of range. Attached is the code. Can
> anyone give some suggesttion?
>
> The Mus musculus Genbank file can be downloaded at :
> ftp://ftp.ncbi.nih.gov/genomes/M_musculus/CHR_02/mm_alt_chr2.gbk.gz
>
> Thanks in advance
>
> Gang
> ==========================================
> public class TestMus {
>   public void testMusChr2() throws FileNotFoundException,
> NoSuchElementException, BioException {
>       String fp="/tmp/mm_alt_chr2.gbk";
>       System.out.println("File: " + fp);
>       BufferedReader gReader = new BufferedReader(new InputStreamReader(new
> FileInputStream(new File(fp))));
>       Namespace ns = (Namespace) RichObjectFactory.getDefaultNamespace();
>       RichSequenceIterator seqI =
> RichSequence.IOTools.readGenbankDNA(gReader, ns);
>       while (seqI.hasNext()) {
>           RichSequence seq = seqI.nextRichSequence();
>           String organism = seq.getTaxon().getDisplayName();
>           String accession = seq.getAccession();
>           String identifier = seq.getIdentifier();
>           int taxonID = seq.getTaxon().getNCBITaxID();
>           String division = seq.getDivision();
>           String seqVersion = "" + seq.getSeqVersion();
>           int seqLength = seq.length();
>           String description = seq.getDescription();
>           System.out.println("Organism: " + organism
>                   + "\nAccession: " + accession
>                   + "\nIdentifier: " + identifier
>                   + "\nTaxonID: " + taxonID
>                   + "\nDivision: " + division
>                   + "\nSeqVersion: " + seqVersion
>                   + "\nLength: " + seqLength);
>           System.out.println("2041-2101: " + seq.subStr(2041, 2101));
>           for (Iterator i = seq.features(); i.hasNext();) {
>               RichFeature f = (RichFeature) i.next();
>               int rank = f.getRank();
>               String fType = f.getType();
>               if (fType.toLowerCase().equals("gene")) {
>                   int startPos=f.getLocation().getMin();
>                   int endPos=f.getLocation().getMax();
>                   int geneLen=endPos-startPos+1;
>                   String sequence=seq.subStr(startPos, endPos);
>                   String strand = f.getStrand().getToken() + "";
>                   Annotation ann = (Annotation) f.getAnnotation();
>                   String geneIdentifier ="";
>                   if (ann.containsProperty("locus_tag")) {
>                       geneIdentifier=ann.getProperty("locus_tag") + "";
>                   }
>                   else geneIdentifier=ann.getProperty("gene") + "";
>
>                   String alternativeIdentifiers="";
>                   try {
>                       alternativeIdentifiers= (String)
> ann.getProperty("gene");
>
>                   } catch(NoSuchElementException e) {}
>                   String annotation="";
>                   System.out.println(rank + "\t" + geneIdentifier + "\t" +
> alternativeIdentifiers + "\t"
>                           + startPos + "\t" + endPos + "\t" + geneLen +
> "\t" + strand);
>               }
>           }
>       }
>   }
>   public static void main(String [] args) throws Exception {
>      TestMus tm=new TestMus();
>       tm.testMusChr2();
>   }
> }
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