[Biojava-dev] read fasta file

[Mark Schreiber]

Along these lines I have plans to add a way to format the Fasta header
in the RichSequence.IOTools so that the content of it can be
customised. Currently it follows the NCBI model and tries to add
everything it can.

I would be interested in proposals for a template mechanism.

- Mark

On Jan 8, 2008 4:51 PM, Richard Holland <holland at ebi.ac.uk> wrote:
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> SeqIOTools is deprecated - this means that it _may_ get dropped in a
> future release and so you can't rely on it being present in any future
> release.
>
> RichSequence.IOTools follows the FASTA format exactly, which requires a
> namespace prefix in the header, and it will change the existing header
> if it does not already meet the FASTA standard. There is currently no
> way to stop it from doing that, although you might want to raise a bug
> report so that it goes on our list of things to change. You can do that
> here: http://bugzilla.open-bio.org/enter_bug.cgi?product=BioJava
>
> cheers,
> Richard
>
>
> Michael Gang wrote:
> > Dear All,
> >
> > I want to read a fasta file of dna (the accessions are internal to our
> > company and may not be like the convention), make manipulations on it
> > and write it to another file.
> > When i take the example from the book "Biojava in Anger" it works
> > fine, but I get warnings that the SeqIOTools type is deprecated.
> > When using the RichSequence.IOTools package I have problems that when
> > writing the fasta it changes the fasta header (it adds the lcl:
> > prefix).
> > I want that the fasta header will be in the output file like in the input file.
> > Will the SeqIOTools type supported further ?
> > If not, is there another way to solve the problem ?
> >
> > Thanks in advance,
> > Michael
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
>
> - --
> Richard Holland (BioMart)
> EMBL EBI, Wellcome Trust Genome Campus,
> Hinxton, Cambridgeshire CB10 1SD, UK
> Tel. +44 (0)1223 494416
>
> http://www.biomart.org/
> http://www.biojava.org/
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