/ 
BioPerl-Run-1.007003
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::EMBOSSacd

NAME

Bio::Tools::Run::EMBOSSacd - class for EMBOSS Application qualifiers

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 EMBOSSacd represents all the possible command line arguments that can be given to an EMBOSS application.

Do not create this object directly. It will be created and attached to its corresponding Bio::Tools::Run::EMBOSSApplication if you set

$application->verbose > 0

Call

$application->acd

to retrive the Bio::Tools::Run::EMBOSSApplication::EMBOSSacd object.

See also Bio::Tools::Run::EMBOSSApplication and 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://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 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 _

new

Title   : new
Usage   : $emboss_prog->acd($prog_name);
Function: Constructor for the class.
          Calls EMBOSS program 'acdc', converts the
          HTML output into XML and uses XML::Twig XML
          parser to write out a hash of qualifiers which is
          then blessed.
Throws  : without program name
Returns : new object
Args    : EMBOSS program name

name

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

print

Title   : print
Usage   : $embossacd->print; $embossacd->print('-word');
Function: Print out the qualifiers.
          Uses Data::Dumper to print the qualifiers into STDOUT.
          A valid qualifier name given as an argment limits the output.
Throws  :
Returns : print string
Args    : optional qualifier name

mandatory

Title   : mandatory
Usage   : $acd->mandatory
Function: gets a  mandatory subset of qualifiers
Throws  :
Returns : Bio::Tools::Run::EMBOSSacd object
Args    : none

Qualifier queries

These methods can be used test qualifier names and read values.

qualifier

Title   : qualifier
Usage   : $acd->qualifier($string)
Function: tests for the existence of the qualifier
Throws  :
Returns : boolean
Args    : string, name of the qualifier

category

Title   : category
Usage   : $acd->category($qual_name)
Function: Return the category of the qualifier
Throws  :
Returns : 'mandatory' or 'optional' or 'advanced' or
           'associated' or 'general'
Args    : string, name of the qualifier

values

Title   : values
Usage   : $acd->values($qual_name)
Function: Return the possible values for the qualifier
Throws  :
Returns : string
Args    : string, name of the qualifier

descr

Title   : descr
Usage   : $acd->descr($qual_name)
Function: Return the description of the qualifier
Throws  :
Returns : boolean
Args    : string, name of the qualifier

unnamed

Title   : unnamed
Usage   : $acd->unnamed($qual_name)
Function: Find if the qualifier can be left unnamed
Throws  :
Returns : 0 if needs to be named, order number otherwise
Args    : string, name of the qualifier

default

Title   : default
Usage   : $acd->default($qual_name)
Function: Return the default value for the qualifier
Throws  :
Returns : scalar
Args    : string, name of the qualifier