On Fri, Feb 08, 2002 at 03:48:36PM -0500, [EMAIL PROTECTED] wrote:
> Hello
>
> Very new to bioJava site, wondered if methods are available for parsing NCBI
> Genbank information. If possible siting
> examples in the documentation would be appreciated. Any suggestions concerning
> bioJava and NCBI Genbank would
> be welcomed.....
Does the following code fragment do what you want:
BufferedReader stream = new BufferredReader(
new FileReader("some-genbank-file.gb")
) ;
SequenceIterator si = SeqIOTools.readGenbank(stream);
while (si.hasNext()) {
Sequence seq = si.nextSequence();
// Your processing here...
}
That should work both with 1.1x releases and with 1.2rc1.
If you're just starting, I'd actually recommend you look
at 1.2 -- the project has moved on a long way since the
1.1 releases.
For more information about reading and writing sequence
files, look at:
http://www.biojava.org/tutorials/chap_iobasics.html
Or the JavaDoc documentation for the package
org.biojava.bio.seq.io
Hope this helps,
Thomas.
_______________________________________________
Biojava-l mailing list - [EMAIL PROTECTED]
http://biojava.org/mailman/listinfo/biojava-l
