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

Bernd Web bernd.web at gmail.com
Wed Sep 13 07:54:53 EDT 2006


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/Bio/Factory/EMBOSS.html
(and: http://doc.bioperl.org/releases/bioperl-current/bioperl-run/Bio/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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