Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::Tools::Run::EMBOSSacd.3pm

NAME

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

SYNOPSIS

   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
   }
 
 

DESCRIPTION

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
 
 

Call

   $application->acd
 
 

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

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

FEEDBACK

Mailing Lists

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.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

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.

Reporting Bugs

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:

   http://bugzilla.open-bio.org/
 
 

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
 
 

APPENDIX

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

new

  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
 
 

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
 
 

print

  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
 
 

mandatory

  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.

qualifier

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

category

  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
 
 

values

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

descr

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

unnamed

  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
 
 

default

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