[Bioperl-l] Puzzled...

Brian Osborne osborne1 at optonline.net
Fri Dec 16 18:18:23 EST 2005


The module I have in mind is simple, it queries the Sequence Revision
History page at NCBI and extracts useful information, something like:

    use NCBIRevision;

    my $q = new NCBIRevision;

    my $result = $q->get_history($id);

    # all GIs, which may include the GI used to query
    my @all_gis = $result->get_all();

    # the most recent GI, may or may not be the id used to query
    my $live_gi = $result->get_live();

My perplexity arises when I take a look around and see the different ways
that these sorts of things have been accomplished in Bioperl. WebDBSeqI is
out, this is about constructing Sequence objects from the query results.
SimpleWebAnalysis doesn¹t look exactly right, this is designed to submit
Sequence objects to the Web server and return the results in various ways.
Then we have WebAgent (DB/MeSH, DB/CUTG) and Root::HTTPGet (DB/Taxonomy,
DB/Expression). Of course every one of these is HTTP::Request and
LWP::UserAgent underneath.

Is there a preferred approach? I could just strike out and write this based
on those last 2 modules but that doesn¹t seem right either.

Brian O.

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