/ 
BioPerl-Run-1.007001
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::EMBOSSApplication

NAME

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

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 

  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 EMBOSSApplication class can represent EMBOSS any 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    :