[Bioperl-l] Bioperl 1.5.2 RC2

Chris Fields 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
core distribution.

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
> candidate.

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.  

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign

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