XML support in FASTA?
kdj at fes1.sanger.ac.uk
Tue Sep 18 11:04:05 EST 2001
>>>>> "Greg" == greg quinn <greg.quinn at syngenta.com> writes:
Greg> Does anyone know if there is planned any kind of support in
Greg> the FASTA suite of programs for producing FASTA output in
Greg> XML anytime soon? Does such a beast already exist? Thanks
I don't know about support within Fasta (I just grepped for xml in the
source + docs of the latest version and found no mention, so I assume
nothing is imminent).
I wrote a parser for the -m 10 Fasta format for the BioJava
project. This can be coupled to the project's framework for generating
SAX events to a common DTD for Blast, Fasta and HMMER. There are event
listeners provided which emit XML (no coding required).
See http://biojava.org if you are interested. If it looks useful to
you but you can't find what you need on the site, feel free to drop me
-= Keith James - kdj at sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA
More information about the Bio-soft