[Bioperl-l] Questions from a Bioperl beginner?

Sat Jul 10 11:44:56 EDT 2004

You are probably using a version of bioperl which does not have the
changes to NCBI's BLAST RID names.

If you grab the latest RemoteBlast.pm from CVS http://cvs.open-bio.org or
from the SRC tree http://www.bioperl.org/SRC/
So RemoteBlast.pm is here
 http://www.bioperl.org/SRC/branch-1-4/Bio/Tools/Run/
just drop the latest file in your local distribution.

-jason
On Fri, 9 Jul 2004 jsun at biologicaltargets.com wrote:

> Dear Sir or Madam;
>   I tried to run some small bioperl program after I successfully installed
> Perl and Bioperl in my computer. While I get some problems and need to
> ask for your kind help. I run a pl file as attached below which I copied
> from bptutorial file:
> **************************************************************
> use Bio::Perl;
> use strict;
> use warnings;
>
> my $seq_object = get_sequence('swissprot',"ROA1_HUMAN");
>
>   # uses the default database - nr in this case
> my $blast_result = blast_sequence($seq_object);
>
> write_blast(">roa1.blast",$blast_result);
> *****************************************************************
>
> Since I didn't make any changes to the source code, it should run fine but
> it failed on my computer. And the error message is:
>
> .....
> Submitted Blast for [ROA1_HUMAN]
> ----------------WARNING----------------
> MSG: UNKNOWN
>
> <P><!
> QBlastInfoBegin
> --><p><BODY BGCOLOR="#FFFFFF">
> <hr><front color="red">ERROR: Results for RID
> 1089388321-32330-213160811820 not found</font><hr>
> -----------------------------------
>
> So what's the problem here? and I also tried the
> Bio::Tools::Run::RemoteBlast function, it shows the same error. How can I
> solve this problem? And is there any troubleshooting documents
> that I can use if I get any further problem during my testing?
>
> Your help are the most appreciated.
> Thanks a lot
> Jian Sun
>
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu