[Bioperl-l] Bioperl 1.5.2 RC2

[Sendu Bala]

Niels Larsen wrote:

> ------------ EBI
> 
> I invoked the EBI script
> 
> http://www.ebi.ac.uk/Tools/webservices/downloads/WSWUBlastSOAPLite.zip
> 
> like this
> 
> WSWUBlastClient.pl -p blastn -D embl test.fasta
> 
> where the content of test.fasta is below, and got
> 
> Can't find method element in the message at 
> /ebi/extserv/bin/perl-5.8.3/lib/site_perl/5.8.3/SOAP/Lite.pm line 2311.

As you admit, this is not a Bioperl issue. I would suggest you contact 
EBI support.

In the mean time/alternatively I'd suggest investigating the Bioperl 
interface to the SOAP server, which is part of the Bioperl-run package.

http://doc.bioperl.org/releases/bioperl-current/bioperl-run/Bio/Tools/Run/Analysis.html


> ------------ DDBJ
> 
> Inspired by this page,
> 
> http://xml.nig.ac.jp/doc/Blast.txt
> 
> I made this test script
[snip]
> which for me prints undef.

Again, not something I can really help you with. You'll need to 
triple-check your code and then seek support from the providers of that 
SOAP service.


> ------------- NCBI/Bioperl
> 
> I installed 1.5.2-RC2, looked at the RemoteBlast example in
> 
> http://www.bioperl.org/wiki/Bptutorial.pl
> 
> and then put that into this test code, more or less cut/paste,
[snip]
> Maybe I am supposed to add a check for content in $rc and then stop
> the inner loop?

Yes, the wiki page example isn't really adequate. I'll update it. For a 
better code example see the RemoteBlast documentation:

http://doc.bioperl.org/bioperl-live/Bio/Tools/Run/RemoteBlast.html


> I could figure that out maybe, but I wish there was a
> function which simply takes a single sequence + arguments and only
> returns a list of matches when done, and does not return until then
> (or until a specified timeout).

Yes, I hardly find dealing with RIDs that pleasant. You might like to 
add a feature request to Bugzilla.