Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::Tools::Run::EMBOSSApplication.3pm

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://bugzilla.open-bio.org/
 
 

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    :