/ 
bioperl-1.0.2
/ 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 = new Bio::Factory::EMBOSS
  $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 = new Bio::AlignIO(-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 which primes it by reading in the ADC description of the command line options. See also 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://bio.perl.org/MailList.html             - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

AUTHOR - Heikki Lehvaslaiho

Email: heikki@ebi.ac.uk Address:

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

CONTRIBUTORS

Email: jason@bioperl.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

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

Internal methods

Do not call these methods directly

_acd2input

Title   : _acd2input
Usage   : $embossfactory->_acd2input()
Function: compares ACD file requirements to input hash
Returns : 
Throws  : if requirements are not met 
Args    : None