[Biojava-l] WriteFasta

[Saif Ur-Rehman]

Dear Richard,

I have tried the RichSEquence.IOTools.writeFasta method and this method is still
appending the characters "??" to the front of each write. I am using a 
FileOutputStream and a Sequence object as inputs to the method. like so.


 Sequence seq; // read in from File
 FileOutputStream f =new FileOutputStream (fileName);


			   try{

			    	RichSequence.IOTools.writeFasta(f,
			    	        seq,
			    	        RichObjectFactory.getDefaultNamespace()
			    	        );


			    }


Thanks a lot for your time

Sincerely,

Saif

Quoting Richard Holland <holland at ebi.ac.uk>:

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> SeqIOTools is deprecated.
>
> Try RichSequence.IOTools.writeFasta() instead to see if that helps.
>
> e.g.:
>
> RichSequence.IOTools.writeFasta(
> 	System.out,
> 	seq,
> 	RichObjectFactory.getDefaultNamespace()
> 	);
>
> where seq is either a Sequence or a SequenceIterator.
>
> cheers,
> Richard
>
> Saif Ur-Rehman wrote:
> > Dear All,
> >
> > I was writing to ask about the SeqIOTools.writeFasta() Method. I am
> currently
> > trying to break up Fasta Files of whole organisms into one file per gene
> for
> > further analysis. However the writeFasta method appears to append the
> > characters
> > "¨Ì
> >
> > ------------------------------------------------------------------
> > University of St Andrews Webmail: https://webmail.st-andrews.ac.uk
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
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-------------------------------------------------------------------------------
Saif Ur-Rehman
Research Student
The Centre for Evolution, Genes & Genomics (CEGG)
Dyers Brae
School of Biology
The University of St Andrews
St Andrews,
Fife
Scotland,UK

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University of St Andrews Webmail: https://webmail.st-andrews.ac.uk