[Bioperl-l] Bio::Factory::EMBOSS synopsis

smarkel at scitegic.com smarkel at scitegic.com
Thu Sep 14 15:13:38 EDT 2006


Bernd,

Based on the error message you posted

> ------------- EXCEPTION  -------------
> MSG: Attribute [-seqall] not recognized!

it looks like there's a mismatch between the command-line arguments
you're using via BioPerl and those expected by water.  "water -h"
will give you the correct command-line syntax.

Scott

Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at scitegic.com
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> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Bernd Web
> Sent: Wednesday, 13 September 2006 04:55
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] Bio::Factory::EMBOSS synopsis
> 
> Hi,
> 
> I started to use Bio::Factory::EMBOSS and started with the 
> example in the synopsis.
> Although now I managed to do what I wanted, it seems like the 
> synopsis is not correct.
> See
> http://doc.bioperl.org/releases/bioperl-current/bioperl-run/Bi
o/Factory/EMBOSS.html
> (and: 
> http://doc.bioperl.org/releases/bioperl-current/bioperl-run/Bi
o/Tools/Run/EMBOSSApplication.html)
> for the code.
> 
> I cannot run "water". Using the latest CVS, (Emboss.pm v 1.7) 
> and EMBOSS v 2.9.0, I get wrong output. In the commandline 
> the reference to the ARRAY \@seqs_to_check appears.
> Output is:
> sh: -c: line 1: syntax error near unexpected token `('
> sh: -c: line 1: `water  -gapopen 10.0 -gapextend 0.5 -seqall
> ARRAY(0x8bdb154) -outfile out.water -sequencea aseq -auto'
> 
> When I set $water->verbose(1); the output is:
> $VAR1 = {
>           '-gapopen' => '10.0',
>           '-gapextend' => '0.5',
>           '-seqall' => [
>                          'CKRIHIGPGRAFWTTWC'
>                        ],
>           '-outfile' => 'out.water',
>           '-sequencea' => 'aseq'
>         };
> Input attr: gapopen => 10.0
> Input attr: gapextend => 0.5
> 
> ------------- EXCEPTION  -------------
> MSG: Attribute [-seqall] not recognized!
> 
> STACK Bio::Tools::Run::EMBOSSApplication::run
> /home/bwbrandt/perllib/Bio/Tools/Run/EMBOSSApplication.pm:204
> STACK toplevel emboss_factory.pl:27
> 
> Code is as in the SYNOPSIS but with:
> my $seq_to_test = "aseq"; # this would have a seq here my 
> @seqs_to_check; # this would be a list of seqs to compare
>                      # (could be just 1) $seqs_to_check[0] = 
> "CKRIHIGPGRAFWTTWC";
> 
> Any suggestions what should be coded?
> 
> Thanks,
> Bernd


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