[Bioperl-l] Bioperl 1.5.2 RC2
bix at sendu.me.uk
Wed Oct 18 08:55:21 UTC 2006
Niels Larsen wrote:
> ------------ EBI
> I invoked the EBI script
> 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
In the mean time/alternatively I'd suggest investigating the Bioperl
interface to the SOAP server, which is part of the Bioperl-run package.
> ------------ DDBJ
> Inspired by this page,
> I made this test script
> 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
> ------------- NCBI/Bioperl
> I installed 1.5.2-RC2, looked at the RemoteBlast example in
> and then put that into this test code, more or less cut/paste,
> 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:
> 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.
More information about the Bioperl-l