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ANJAN PURKAYASTHA | 3 Mar 18:31
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problem with Bio::Tools::EMBOSS

hi
i am tried to use the perl wrappers for EMBOSS with:

use lib "/Users/anjan/perl_directory/bioperl-1.5.2_102/";
use Bio::Factory::EMBOSS;

however it seems that Bio::Factory::EMBOSS cannot be found in the bioperl
directory mentioned above.

so i tried to install Bio::Factory::EMBOSS from the cpan website. i got the
attached error message.

any ideas on what i need to do to  make this work?
all advice will be appreciated.

tia,

anjan

--

-- 
ANJAN PURKAYASTHA, PhD.
Senior Computational Biologist
==========================

1101 King Street, Suite 310,
Alexandria, VA 22314.
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703.740.6939 (mobile)

email:
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Chris Fields | 3 Mar 19:54
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Re: problem with Bio::Tools::EMBOSS

You'll need to install bioperl-run.  Bio::Factory::EMBOSS is in  
bioperl-run, not the main bioperl distribution (aka bioperl-core).

chris

On Mar 3, 2008, at 11:31 AM, ANJAN PURKAYASTHA wrote:

> hi
> i am tried to use the perl wrappers for EMBOSS with:
>
> use lib "/Users/anjan/perl_directory/bioperl-1.5.2_102/";
> use Bio::Factory::EMBOSS;
>
> however it seems that Bio::Factory::EMBOSS cannot be found in the  
> bioperl
> directory mentioned above.
>
> so i tried to install Bio::Factory::EMBOSS from the cpan website. i  
> got the
> attached error message.
>
> any ideas on what i need to do to  make this work?
> all advice will be appreciated.
>
> tia,
>
> anjan
>
>
> --
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Dave Messina | 3 Mar 20:34
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Re: problem with Bio::Tools::EMBOSS

Hi Anjan,

Bio::Factory::EMBOSS is not part of the BioPerl core distribution, but
rather part of bioperl-run. For some reason CPAN went for the old (1.4)
version of bioperl-run rather than the current 1.5.2.

And indeed, I seem to run into the same problem:
cpan> d /bioperl/

Distribution    BIRNEY/bioperl-1.2.1.tar.gz
Distribution    BIRNEY/bioperl-1.2.2.tar.gz
Distribution    BIRNEY/bioperl-1.2.3.tar.gz
Distribution    BIRNEY/bioperl-1.2.tar.gz
Distribution    BIRNEY/bioperl-1.4.tar.gz
Distribution    BIRNEY/bioperl-db-0.1.tar.gz
Distribution    BIRNEY/bioperl-ext-1.4.tar.gz
Distribution    BIRNEY/bioperl-gui-0.7.tar.gz
Distribution    BIRNEY/bioperl-run-1.2.2.tar.gz
Distribution    BIRNEY/bioperl-run-1.4.tar.gz
Distribution    BOZO/Fry-Lib-BioPerl-0.15.tar.gz
Distribution    CRAFFI/Bundle-BioPerl-2.1.8.tar.gz
12 items found

but when I ask in a different way the right distributions show up. [Sendu,
any idea what's going on here?]

cpan> ls
SENDU
 5919092 2007-02-14 SENDU/bioperl-1.5.2_102.tar.gz
  320154 2006-12-06 SENDU/bioperl-db-1.5.2_100.tar.gz
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Mauricio Herrera Cuadra | 3 Mar 20:25
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Re: problem with Bio::Tools::EMBOSS

Hi Anjan,

It looks like you are using the latest BioPerl developer release
(bioperl-1.5.2_102) from CPAN, to have Bio::Factory::EMBOSS available
then you should try installing the latest BioPerl-run as well
(bioperl-run-1.5.2_100). After you install it, you'll have to modify
your 'use lib' pragma for your script to work as you expect:

use lib "/Users/anjan/perl_directory/bioperl-run-1.5.2_100/";
use Bio::Factory::EMBOSS;

Hope this helps.

Regards,
Mauricio.

ANJAN PURKAYASTHA wrote:
> hi
> i am tried to use the perl wrappers for EMBOSS with:
> 
> use lib "/Users/anjan/perl_directory/bioperl-1.5.2_102/";
> use Bio::Factory::EMBOSS;
> 
> however it seems that Bio::Factory::EMBOSS cannot be found in the bioperl
> directory mentioned above.
> 
> so i tried to install Bio::Factory::EMBOSS from the cpan website. i got the
> attached error message.
> 
> any ideas on what i need to do to  make this work?
(Continue reading)

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Chris Fields | 3 Mar 21:05
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Re: problem with Bio::Tools::EMBOSS


On Mar 3, 2008, at 1:34 PM, Dave Messina wrote:

> Hi Anjan,
>
> Bio::Factory::EMBOSS is not part of the BioPerl core distribution, but
> rather part of bioperl-run. For some reason CPAN went for the old  
> (1.4)
> version of bioperl-run rather than the current 1.5.2.
>
> And indeed, I seem to run into the same problem:
> cpan> d /bioperl/
>
> Distribution    BIRNEY/bioperl-1.2.1.tar.gz
> Distribution    BIRNEY/bioperl-1.2.2.tar.gz
> Distribution    BIRNEY/bioperl-1.2.3.tar.gz
> Distribution    BIRNEY/bioperl-1.2.tar.gz
> Distribution    BIRNEY/bioperl-1.4.tar.gz
> Distribution    BIRNEY/bioperl-db-0.1.tar.gz
> Distribution    BIRNEY/bioperl-ext-1.4.tar.gz
> Distribution    BIRNEY/bioperl-gui-0.7.tar.gz
> Distribution    BIRNEY/bioperl-run-1.2.2.tar.gz
> Distribution    BIRNEY/bioperl-run-1.4.tar.gz
> Distribution    BOZO/Fry-Lib-BioPerl-0.15.tar.gz
> Distribution    CRAFFI/Bundle-BioPerl-2.1.8.tar.gz
> 12 items found
>
> but when I ask in a different way the right distributions show up.  
> [Sendu,
> any idea what's going on here?]
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ANJAN PURKAYASTHA | 3 Mar 20:57
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Re: problem with Bio::Tools::EMBOSS

guys,
thanks! i got bioperl-run to work.
next question, let's say i want to run the palindrome program in emboss
using the bioperl wrapper.   now, palindrome takes in a list of parameter
values- these are fed into emboss as a key-value hash. where do i find the
correct names of the keys to create the input hash?
tia.

anjan

On Mon, Mar 3, 2008 at 2:25 PM, Mauricio Herrera Cuadra <
arareko <at> campus.iztacala.unam.mx> wrote:

> Hi Anjan,
>
> It looks like you are using the latest BioPerl developer release
> (bioperl-1.5.2_102) from CPAN, to have Bio::Factory::EMBOSS available
> then you should try installing the latest BioPerl-run as well
> (bioperl-run-1.5.2_100). After you install it, you'll have to modify
> your 'use lib' pragma for your script to work as you expect:
>
> use lib "/Users/anjan/perl_directory/bioperl-run-1.5.2_100/";
> use Bio::Factory::EMBOSS;
>
> Hope this helps.
>
> Regards,
> Mauricio.
>
>
(Continue reading)

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Daniel Gerlach | 4 Mar 09:48
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Bio::TreeIO rises error "Weak references are not implemented in the version of perl"

Hello,

Trying to run Bio::TreeIO by this command:

perl -e 'use Bio::TreeIO'

I get the following error:

Weak references are not implemented in the version of perl at 
/usr/lib/perl5/site_perl/5.8.8/Bio/Tree/Node.pm line 76
BEGIN failed--compilation aborted at 
/usr/lib/perl5/site_perl/5.8.8/Bio/Tree/Node.pm line 76.
Compilation failed in require at 
/usr/lib/perl5/site_perl/5.8.8/Bio/TreeIO/TreeEventBuilder.pm line 65.
BEGIN failed--compilation aborted at 
/usr/lib/perl5/site_perl/5.8.8/Bio/TreeIO/TreeEventBuilder.pm line 65.
Compilation failed in require at 
/usr/lib/perl5/site_perl/5.8.8/Bio/TreeIO.pm line 77.
BEGIN failed--compilation aborted at 
/usr/lib/perl5/site_perl/5.8.8/Bio/TreeIO.pm line 77.
Compilation failed in require at -e line 1.
BEGIN failed--compilation aborted at -e line 1.

I am running perl v5.8.8 on Fedora 8 on a 64bit machine. I installed a 
recent version of bioperl around 5 month ago. Any suggestions of why 
this module can't be loaded correctly?

Greetings, Daniel
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Sendu Bala | 4 Mar 12:55
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Re: Bio::TreeIO rises error "Weak references are not implemented in the version of perl"

Daniel Gerlach wrote:
> Hello,
> 
> Trying to run Bio::TreeIO by this command:
> 
> perl -e 'use Bio::TreeIO'
> 
> I get the following error:
> 
> Weak references are not implemented in the version of perl 
> [...]
> I am running perl v5.8.8 on Fedora 8 on a 64bit machine. I installed a 
> recent version of bioperl around 5 month ago. Any suggestions of why 
> this module can't be loaded correctly?

Redhat/Fedora apparently has Perl issues.

First try installing the latest version of Scalar::Util yourself:

perl -MCPAN -e shell
force install Scalar::Util

If that doesn't work, you'll have to download and compile Perl yourself 
from source (don't use Fedora's installation system).
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Alexie Papanicolaou | 4 Mar 13:03
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Bio/SearchIO/Writer/GbrowseGFF.pm

hello all,

1) I was wondering if you would you know what this error means and had 
time to help...

Use of uninitialized value in concatenation (.) or string at 
/usr/local/share/perl/5.8.8/Bio/SearchIO/Writer/GbrowseGFF.pm line 287

line 287 is
            else {
                $tags{'Target'} = "$prefix:$seqname $qpmax $qpmin";
            }

this is the header
# $Id: GbrowseGFF.pm,v 1.15.4.1 2006/10/02 23:10:27 sendu Exp $
#
# BioPerl module Bio::SearchIO::Writer::GbrowseGFF.pm

this is how I call it... ( 2.6.18-6-amd64, x86_64, perl, v5.8.8, 
bioperl: tried with both 1.5.2_102 from cvs and checked out svn version 
today)

use Bio::SearchIO::Writer::GbrowseGFF;
use Bio::SearchIO;
if ($program eq "blastn"){
#my $out_gff  = new Bio::SearchIO(-writer => $writer_gff,
 my $out_gff = new Bio::SearchIO(-output_format  => 'GbrowseGFF',
                        -output_cigar   => 1,
                        -output_signif  => 1,
                        -file   => ">$infile.$query.blast.gff");
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Alexie Papanicolaou | 4 Mar 13:04
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Gbrowse.pm followup

Oh the iD bug is fixed in the svn developer branch.

ta
a

--

-- 
--
Alexie Papanicolaou
Entomology
Max Planck Institute for Chemical Ecology
Hans Knoell Str 8
Jena 07745
Germany
Email apapanicolaou <at> ice.mpg.de
Tel +493641571561
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Gmane