NAME

Bio::Tools::Run::EMBOSSApplication - class for EMBOSS Applications

SYNOPSIS

  # 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
  }

DESCRIPTION

The EMBOSSApplication class can represent any EMBOSS program. It is created by a Bio::Factory::EMBOSS object.

If you want to check command line options before sending them to the program set $prog->verbose to positive integer. The ADC description of the available command line options is then parsed in and compared to input.

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

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org

CONTRIBUTORS

Email: jason-AT-bioperl_DOT_org

APPENDIX

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

run

 Title   : run
 Usage   : $embossapplication->run($attribute_hash)
 Function: Runs the EMBOSS program.
 Returns : string or creates files for now; will return objects!
 Args    : hash of input to the program

acd

 Title   : acd
 Usage   : $embossprogram->acd
 Function: finds out all the possible qualifiers for this
           EMBOSS application. They can be used to debug the
           options given.
 Throws  :
 Returns : boolean
 Args    :

name

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

descr

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

group

 Title   : group
 Usage   : $embossprogram->group
 Function: sets/gets the group of the EMBOSS program
           Setting is done by the EMBOSSFactory object,
           you should only get it.

           If the application is assigned into a subgroup
           use l<subgroup> to get it.
 Throws  :
 Returns : string, group name
 Args    : group string

subgroup

 Title   : subgroup
 Usage   : $embossprogram->subgroup
 Function: sets/gets the subgroup of the EMBOSS program
           Setting is done by the EMBOSSFactory object,
           you should only get it.
 Throws  :
 Returns : string, subgroup name; undef if not defined
 Args    : None

program_dir

 Title   : program_dir
 Usage   :
 Function: Required by WrapperBase
 Throws  :
 Returns : Name of directory with EMBOSS programs
 Args    :

program_path

 Title   : program_path
 Usage   :
 Function: Required by WrapperBase
 Throws  :
 Returns : Full path of program
 Args    :

executable

 Title   : executable
 Usage   :
 Function: Required by WrapperBase
 Throws  :
 Returns : Name of program
 Args    :