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

Brian Osborne osborne1 at optonline.net
Thu Sep 14 22:43:24 EDT 2006


Scott and Bernd,

The names of the parameters passed to EMBOSS applications have changed over
the past EMBOSS versions, Bioperl handles older versions. Some discussion:

http://article.gmane.org/gmane.comp.lang.perl.bio.general/7682/match=emboss

Bernd, what version EMBOSS are you using?

Brian O.


On 9/14/06 6:17 PM, "Bernd Web" <bernd.web at gmail.com> wrote:

> Hi Scott,
> 
> Thanks. I also thought of the possibility that the emboss module did
> some extra work (due to @seqs_to_check). From the synopsis I thought
> that emboss.pm produced a database from the sequences (or sequence
> files) in the  array. This is not the case. The ARRAY() ref is printed
> to the command line causing the shell errors.
> 
> The following comments in the SYNOPSIS are confusing to me:
> my $seq_to_test; # this would have a seq here
> my @seqs_to_check; # this would be a list of seqs to compare
>                      # (could be just 1)
> 
> Both should be a sequence fileNAMES and the \@seqs_to_check cannot be
> passed (in my hands). It works when passing filenames (one with 1 seq,
> 1 with more than one).
> 
> water->run({ '-asequence' => $seq_to_test, #filename!
>               '-bsequence'    => $seqs_to_check, #filename!
>               '-gapopen'   => '10.0',
>               '-gapextend' => '0.5',
>               '-outfile'   => $wateroutfile});
> 
> It would be clearer (to me at least) to adapt the synopsis (if the
> above is indeed the only way to run water).
> 
> Bernd
> 
> On 9/14/06, smarkel at scitegic.com <smarkel at scitegic.com> wrote:
>> 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
>> SciTegic Inc.                       mobile: +1 858 205 3653
>> 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
>> San Diego, CA 92121                 fax:    +1 858 279 8804
>> USA                                 web:    http://www.scitegic.com
>> 
>> 
>> 
>> 
>>> -----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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