Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Contact Us
Online Help
Domain Status
Man Pages

Virtual Servers

Topology Map

Server Agreement
Year 2038

USA Flag



Man Pages
Bio::Tools::Run::EMBOSSacd(3) User Contributed Perl Documentation Bio::Tools::Run::EMBOSSacd(3)

Bio::Tools::Run::EMBOSSacd - class for EMBOSS Application qualifiers

  # Get an EMBOSS factory
  use Bio::Factory::EMBOSS;
  $f = Bio::Factory::EMBOSS -> new();
  # Get an EMBOSS application  object from the factory
  $water = $f->program('water') || die "Program not found!\n";
  # Here is an example of running the application - water can
  # compare 1 sequence against 1 or more sequences using Smith-Waterman.
  # Pass a Sequence object and a reference to an array of objects.
  my $wateroutfile = 'out.water';
  $water->run({-asequence => $seq_object,
               -bsequence => \@seq_objects,
               -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.

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated.                  - General discussion  - About the mailing lists

Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

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

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
2019-01-02 perl v5.28.1

Search for    or go to Top of page |  Section 3 |  Main Index

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with ManDoc.