[Bioperl-l] Puzzled...

Heikki Lehvaslaiho 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:
> Bioperl-l,
> 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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> Bioperl-l at portal.open-bio.org
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     _/  _/  _/  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
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