/ 
bioperl-1.2.3
/ Bio::Factory::EMBOSS

NAME

Bio::Factory::EMBOSS - EMBOSS appliaction factory class

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');

  # 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 EMBOSS factory class encapsulates access to EMBOSS programs. A factory object allows creation of only known applications.

If you want to check command line options before sending them to the program set $factory->verbose to positive integer. The value is passed on to programs objects and the ADC description of the available command line options is parsed and compared to input.

See also Bio::Tools::Run::EMBOSSApplication 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://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://bugzilla.bioperl.org/

AUTHOR - Heikki Lehvaslaiho

Email: heikki@ebi.ac.uk 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 _

location

Title   : location
Usage   : $embossfactory->location
Function: get/set the location of EMBOSS programs.
          Valid values are 'local' and 'novella'.
Returns : string, defaults to 'local'
Args    : string

program

Title   : program
Usage   : $embossfactory->program('program_name')
Function: Creates a representation of a single EMBOSS program
Returns : Bio::Tools::Run::EMBOSSApplication object
Args    : string, program name

version

Title   : $self->version
Usage   : $embossfactory->version()
Function: gets the version of EMBOSS programs
Throws  : if EMBOSS suite is not accessible
Returns : version value
Args    : None

Programs

These methods allow the programmer to query the EMBOSS suite and find out which program names can be used and what arguments can be used.

program_info

Title   : program_info
Usage   : $embossfactory->program_info('emma')
Function: Finds out if the program is available.
Returns : definition string of the program, undef if program name not known
Args    : string, prgramname

Internal methods

Do not call these methods directly

_program_list

Title   : _program_list
Usage   : $embossfactory->_program_list()
Function: Finds out what programs are available.
          Writes the names into an internal hash.
Returns : true if successful
Args    : None