[Biojava-dev] read fasta file

[Richard Holland]

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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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