[Bioperl-l] Hi! everyone

Chris Fields cjfields at uiuc.edu
Tue Mar 21 11:35:03 EST 2006


> -----Original Message-----
> From: r93626012 at ntu.edu.tw [mailto:r93626012 at ntu.edu.tw]
> Sent: Tuesday, March 21, 2006 10:23 AM
> To: Chris Fields
> Subject: RE: [Bioperl-l] Hi! everyone
> 
> Quoting Chris Fields <cjfields at uiuc.edu>:
> 
> Sorry! I forget to tell you that i ran the program on Suse Linux, and
> my bioperl version is 1.4. Is it still has to update or it should work
> without problems on this version? thank you very much!

Please respond to the list as well so that anyone following this thread
might find a resolution to this issue.

In short, yes, update to the newest version of bioperl (1.5.1).  Although it
is a developer version many changes have been added (including critical ones
to SearchIO, RemoteBlast, and SeqIO).  I believe that bioperl 1.4 is about
two years old now; I'm not sure when the push will begin for the next stable
release.  Anyway, try v 1.5.1 first since it should be more stable than a
CVS bleeding edge version.  If that doesn't help try installing from CVS.  

BTW, haven't tried this script on OS X yet with the latest CVS.  We have a
bit of a snowstorm slowing us down up here.  Should be able to get to that
tonight or tomorrow.

Chris


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




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




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