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

[Bernd Web]

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
>