[Bioperl-l] Unigene proposal and basic implementation

[Andrew Macgregor]

Ewan Birney wrote:

> Could you describe (before you check them in) a little more detail - terse
> is fine

OK, here's the outline of what I have at the moment. I'm sure the modules
will be a little rough around the edges, but that's one reason I'd like to
get them out to other people that may want to use them, for some feedback.

If the namespace is more or less agreed who do I see for a cvs account to
check them in so people can take a look?

-- Andrew.

Bio::Cluster::UniGene.pm
    new() - standard new call
    unigene_id() - set/get unigene_id
    title() - set/get title (description)
    gene() - set/get gene
    cytoband() - set/get cytoband
    locuslink() - set/get locuslink
    gnm_terminus() - set/get gnm_terminus
    chromosome() - set/get chromosome
    scount() - set/get scount
    express() - set/get express, takes/returns a reference to an array of
expressed tissues
    next_express() - returns the next tissue expression from an expressed
tissue array
    sts() - set/get sts, takes/returns a reference to an array of sts lines
    next_sts() - returns the next sts line from the array of sts lines
    txmap() - set/get txmap, takes/returns a reference to an array of txmap
lines
    next_txmap() - returns the next txmap line from the array of txmap lines
    protsim() - set/get protsim, takes/returns a reference to an array of
protsim lines
    next_protsim() - returns the next protsim line from the array of protsim
lines
    sequence() - set/get sequence, takes/returns a reference to an array of
references to seq info
    next_seq() - returns a Seq object that currently only contains an
accession number


Bio::ClusterIO::UniGeneIO.pm
    _load_format_module
    _guess_format - both more or less from SeqIO


Bio::ClusterIO::UniGeneIO::unigene.pm
    next_unigene - returns the next unigene in the stream
    
    This module uses Damian Conway's Parse::RecDescent. I know this is not
    everyone's cup of tea but it works well for me, apart from speed. Still
    as was pointed out on the list a few days back, Damian is promising
    Parse::FastDescent this year so I'll upgrade once it's available!