[Biojava-l] GEO SOFT-file parser?

[Keith James]

>>>>> "Petri" == Petri Pehkonen <pehkonen@hytti.uku.fi> writes:

    Petri> Hi, Does there exist any parser that can parse SOFT-files
    Petri> of NCBI's Gene Expression Omnibus database?

Not exactly. However if you are a Java developer there is a toolkit
for quickly creating parsers for tag-value file formats like SOFT. See
the org.biojava.bio.program.tagvalue package.

I wanted a parser for REBASE (format #31) files which have a similar
structure. See org.biojava.bio.molbio.RestrictionEnzymeManager for an
implementation using the tagvalue package (in development CVS HEAD).

    Petri> I would be also interested in parser for Medline-abstract
    Petri> files.

Sorry, I can't help with this one.

Keith

-- 

-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK