[Biojava-l] : prob in reading sequence

Richard Holland holland at eaglegenomics.com
Wed Jun 24 09:36:34 UTC 2009

readEmbl() is for reading EMBL format files. It's not suprising it
causes problems if you use it to try to read Genbank or FASTA!

Also, SeqIOTools is deprecated and not really supported any more. You
should take a look at RichSequence.IOTools instead:



On Wed, 2009-06-24 at 14:59 +0530, ranjith kurungadam wrote:
> hello
> //rof :  m new to this community..
> going on wit my final semester M.Sc project work. m trying to do some
> nucleotide sequence manipulation using biojava.
> //rof : while trying to read different bio formats i found that the method
> SeqIOTools.readEmbl( ) method instantiates the SequenceIterator object with
> some unknown values wen a genbank format is read, but its ok wen a fasta is
> read as stream.hasnext( ) gives Exception.
> i got confused as this is not the case wit other methods readFastaDNA( ) and
> readGenbank( )..
> //Expecting ur support
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Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com

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