[Biojava-l] failed to read genbank peptide file

[Hongyu Zhang]

Thanks for the help, Bruno. But I am able to compile and run the
version of the code that reads nucleotide sequences, plus I can run
all sorts of other methods of biojava without problems, therefore,
the possibility that you suggested is slim.

--
Hongyu Zhang
Computational biologist
Ceres Inc.



Quoting Bruno Aranda - Dev <bruno_dev at ebiointel.com>:

> Welcome then to the Biojava community!
>
> I think you have a corrupt Biojava library (biojava.jar) or maybe
> there
> are resources missing in the classpath. What you should do is:
>
> - Download the latest binary snapshot of Biojava from
> http://www.derkholm.net/autobuild/binaries/
>
> - Check that you put all the libraries needed in the classpath:
>
> java -cp /path/to/one/jar:/path/to/another/jar ReadGB input_file
>
> (also you can have those jars in the CLASSPATH environment
> variable.
>
> You should put the jars explained at
> http://biojava.org/download14.html
>
> After reading the file successfully you will get a Sequence
> object... you
> can try to just print the sequence name (in this case the accession
> number) just using:
>
> String seqName = seq.getName();
> System.out.println(seqName);
>
> and there are many other (and sophisticated) possibilities, of
> course!
>
> Good luck,
>
> Bruno
>
>
>
>