[Bioperl-l] DB::GenBank.pm etc. and net entrez queries

[Hilmar Lapp]

"chris.dag" wrote:
> 
> I was fooling around with scripts/bpfetch.pl and DB::GenBank.pm and saw
> that Entrez has changed the way they want HTTP post requests to be formatted:
> 
> Regarding our branch-06 that we are prepping for a 0.6.1 bugfix release:
> 
> o Do we do nothing since stuff appears to work still?
> o Do we change the base URL to the remapper at qmap.cgi base (very easy to do)

Personally, I'd say if something is not broken then don't fix it. In
particular for the branch.

For the main trunk, at least switching to the mapper is probably
advisable. 

> o Do we change everything and use the new URL/command string structure?
> 

Well, there appears to be a little problem with this, because at least
how I understand it the query 'semantics' changed. With the new command
structure, you're supposed to search for UIDs first, and only then you
can retrieve entries in the format you wish. For instance, accession
numbers are not UIDs. So, you would have two queries running behind the
scenes. 

> 
> Also-- in our CVS head and bioperl-07 release are we going to take out the
> handcoded HTTP stuff and formally transition over to using the Net::
> modules? At the very least that will get rid of the problems that
> behind-the-firewall people have been having since the libnet has good proxy
> code already.
> 

To which Net:: modules are you referring? The ones that came with my
5.005 installation probably won't help in this regard.

This is certainly something that needs to be dealt with. The
Bio::Root::NetManager question I asked in another email is related to
this.

	Hilmar

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Hilmar Lapp                                email: hlapp@gmx.net
NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
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