heikki.lehvaslaiho at gmail.com
Sun Dec 18 16:28:58 EST 2005
Bio::WebDBSeqI is, like you said for retrieving sequences. This is the oldest
code of the lot. A good rewrite has been asked for years.
Bio::Root::HTTPGet does not depend on LWP::UserAgent but duplicates core
functionality, see the docs..
Bio::WebAgent adds bioperl idioms into LWP::UserAgent and is meant to be used
as a basis of more specific implementations.
Bio::Tools::Analysis::SimpleAnalysisBase is a base class for doing Web based
sequence analysis. It is based on Bio::WebAgent and implements
If you need to create something new, base it either on Bio::Root::HTTPGet or
Bio::WebAgent or even better: to use primarily Bio::WebAgent but fall back to
Bio::Root::HTTPGet if LWP::Useragent is not present.
I do not want to complicate matters, but do have a look at
It would be great if the bioperl implementation of nucleotide sequence version
retrieval could be as generic and complete as possible ;-) .
On Saturday 17 December 2005 01:18, Brian Osborne wrote:
> 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.
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
______ _/ _/_____________________________________________________
_/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za
_/_/_/_/_/ Associate Professor skype: heikki_lehvaslaiho
_/ _/ _/ SANBI, South African National Bioinformatics Institute
_/ _/ _/ University of the Western Cape, South Africa
_/ Phone: +27 21 959 2096 FAX: +27 21 959 2512
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