[Bioperl-l] Bioperl 1.5.2 RC2
cjfields at uiuc.edu
Tue Oct 17 15:07:49 UTC 2006
> Niels Larsen wrote:
> > Greetings,
> > I am no perl beginner, but I am a BioPerl beginner. Today I looked
> > for remote similarity services that can be used from Perl. I found
> > the EBI SOAP interface where their example script returns
> > 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.
> What script exactly? There was a problem with the SOAP server that was
> fixed earlier today.
> > and the DDBJ service which (from Denmark) returns
> > undef
> What returned undef? Specifics please.
The first problem, like Sendu mentions, was fixed on the remote server (I
get them to pass now). Those were from bioperl-run, though, not the bioperl
As for DDBJ, do you mean EBI or SwissProt? I ask b/c you mention Denmark.
EBI were having server maintenance outages yesterday, which was announced
As Sendu mentions, please be more specific.
> > and then the NCBI server accessed through BioPerls RemoteBlast which
> > seems to spin in a loop that fills TMPDIR with many tempfiles. Will
> > release 1.5.2 include improvements to RemoteBlast? (I see Roger Hall
> > is working towards that).
> What version of Bioperl were you testing with? What did you do to get it
> to 'spin in a loop'? I can tell you that remote blasting certainly works
> in Bioperl 1.5.2, but you'll have to give more details on the things you
> tried and the problems you encountered.
> You can also answer the questions yourself by trying the release
The tempfiles showing up are from the repeated RID requests and are deleted
after the BLAST run (at least they should be); this is quite normal. They
don't 'spin in a loop' unless the BLAST query is taking a particularly long
time, which can happen depending on how the BLAST query is set up, i.e. what
type of BLAST program is requested, if comp-based stats are requested,
length of query, database requested, etc.
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign
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