[Bioperl-l] Hi! everyone

Chris Fields cjfields at uiuc.edu
Mon Mar 20 13:36:37 EST 2006

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Sunday, March 19, 2006 6:10 PM
> To: r93626012 at ntu.edu.tw
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Hi! everyone
> On Mar 19, 2006, at 8:39 AM, r93626012 at ntu.edu.tw wrote:
> >  Hi!I am a graduate student of National Taiwan University. My name
> > is scott. I had some probelms when i using bioperl module. I wanted
> > to get a sequence from "swissprot" database and blast with nr
> > database of NCBI automatically by bioperl module. This is my program:
> >
> > #!/usr/bin/perl -w
> > use strict;
> > use Bio::Perl;
> >
> > my $seq_object = get_sequence('swissport',"ROA1_HUMAN");
> 'swissport' should be 'swissprot', though I get this script to work
> when spelled either way (well, I get some BLAST results back).  This
> error was, I believe, fixed in a recent version of Bioperl; I would
> upgrade from CVS.   However, the major problem I see is that the
> formatting from Bioperl is completely messed up now; it looks like
> the entire BLAST report is globbed together at the 'Query=' line.
> I'm sure this is an issue related to the recent blast changes at
> NCBI.  I'll look into this tomorrow.
> Chris

To follow up on this (for the mail-list in case anybody comes across this in
the future):

I get this to work without problems on Windows (which is where problems
usually show up).  I'll play around with it a bit more with Mac OS X to see
if this may be an OS issue, but I haven't updated bioperl from CVS on my
wife's IBook in quite a while so it could be an old version of bioperl
mucking up the works.

If this script isn't working for your bioperl version, try installing
bioperl from CVS.  My WinXP is running off bioperl from the latest CVS and
it works fine.


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

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