Bio::Tools::Run::EMBOSSacd(3pm) User Contributed Perl Documentation Bio::Tools::Run::EMBOSSacd(3pm)
NAME
Bio::Tools::Run::EMBOSSacd - class for EMBOSS Application qualifiers
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 . "
";
$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 = 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
perl v5.12.3 2011-06-18 Bio::Tools::Run::EMBOSSacd(3pm)