| Bio::Tools::Run::EMBOSSacd(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::EMBOSSacd(3pm) |
Bio::Tools::Run::EMBOSSacd - class for EMBOSS Application qualifiers
# 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
}
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.
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
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.
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/
Email: heikki-at-bioperl-dot-org Address:
EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
Title : mandatory Usage : $acd->mandatory Function: gets a mandatory subset of qualifiers Throws : Returns : Bio::Tools::Run::EMBOSSacd object Args : none
These methods can be used test qualifier names and read values.
Title : qualifier Usage : $acd->qualifier($string) Function: tests for the existence of the qualifier Throws : Returns : boolean Args : string, name of the qualifier
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
Title : values Usage : $acd->values($qual_name) Function: Return the possible values for the qualifier Throws : Returns : string Args : string, name of the qualifier
Title : descr Usage : $acd->descr($qual_name) Function: Return the description of the qualifier Throws : Returns : boolean Args : string, name of the qualifier
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
Title : default Usage : $acd->default($qual_name) Function: Return the default value for the qualifier Throws : Returns : scalar Args : string, name of the qualifier
| 2018-09-14 | perl v5.26.2 |