Thanks Mark. I did parse out the sequence block with sed and the length
agrees with what the Genbank says.
Gang
Mark Schreiber wrote:
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 <[email protected]
<mailto:[email protected]>> 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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