Bio::Tools::Run::EMBOSSacd(3) class for EMBOSS Application qualifiers


use Bio::Factory::EMBOSS;
# get an EMBOSS application object from the EMBOSS factory
$factory = Bio::Factory::EMBOSS->new();
$application = $factory->program('embossversion');
# run the application with an optional hash containing parameters
$result = $application->run(); # returns a string or creates a file
print $result . "\n";
$water = $factory->program('water');
# here is an example of running the application
# water can compare 1 seq against 1->many sequences
# in a database using Smith-Waterman
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)
my $wateroutfile = 'out.water';
$water->run({ -sequencea => $seq_to_test,
-seqall => \@seqs_to_check,
-gapopen => '10.0',
-gapextend => '0.5',
-outfile => $wateroutfile});
# now you might want to get the alignment
use Bio::AlignIO;
my $alnin = Bio::AlignIO->new(-format => 'emboss',
-file => $wateroutfile);
while( my $aln = $alnin->next_aln ) {
# process the alignment -- these will be Bio::SimpleAlign objects


The EMBOSSacd represents all the possible command line arguments that can be given to an EMBOSS application.

Do not create this object directly. It will be created and attached to its corresponding Bio::Tools::Run::EMBOSSApplication if you set

  $application->verbose > 0



to retrive the Bio::Tools::Run::EMBOSSApplication::EMBOSSacd object.

See also Bio::Tools::Run::EMBOSSApplication and Bio::Factory::EMBOSS.


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AUTHOR - Heikki Lehvaslaiho

Email: heikki-at-bioperl-dot-org Address:

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : $emboss_prog->acd($prog_name);
 Function: Constructor for the class.
           Calls EMBOSS program 'acdc', converts the
           HTML output into XML and uses XML::Twig XML 
           parser to write out a hash of qualifiers which is
           then blessed.
 Throws  : without program name
 Returns : new object
 Args    : EMBOSS program name


 Title   : name
 Usage   : $embossacd->name
 Function: sets/gets the name of the EMBOSS program
           Setting is done by the EMBOSSApplication object,
           you should only get it.
 Throws  : 
 Returns : name string
 Args    : None


 Title   : print
 Usage   : $embossacd->print; $embossacd->print('-word');
 Function: Print out the qualifiers.
           Uses Data::Dumper to print the qualifiers into STDOUT.
           A valid qualifier name given as an argment limits the output.
 Throws  : 
 Returns : print string
 Args    : optional qualifier name


 Title   : mandatory
 Usage   : $acd->mandatory
 Function: gets a  mandatory subset of qualifiers
 Throws  : 
 Returns : Bio::Tools::Run::EMBOSSacd object
 Args    : none

Qualifier queries

These methods can be used test qualifier names and read values.


 Title   : qualifier
 Usage   : $acd->qualifier($string)
 Function: tests for the existence of the qualifier
 Throws  : 
 Returns : boolean
 Args    : string, name of the qualifier


 Title   : category
 Usage   : $acd->category($qual_name)
 Function: Return the category of the qualifier
 Throws  : 
 Returns : 'mandatory' or 'optional' or 'advanced' or 
            'associated' or 'general'
 Args    : string, name of the qualifier


 Title   : values
 Usage   : $acd->values($qual_name)
 Function: Return the possible values for the qualifier
 Throws  : 
 Returns : string
 Args    : string, name of the qualifier


 Title   : descr
 Usage   : $acd->descr($qual_name)
 Function: Return the description of the qualifier
 Throws  : 
 Returns : boolean
 Args    : string, name of the qualifier


 Title   : unnamed
 Usage   : $acd->unnamed($qual_name)
 Function: Find if the qualifier can be left unnamed
 Throws  : 
 Returns : 0 if needs to be named, order number otherwise
 Args    : string, name of the qualifier


 Title   : default
 Usage   : $acd->default($qual_name)
 Function: Return the default value for the qualifier
 Throws  : 
 Returns : scalar
 Args    : string, name of the qualifier