Bio::Tools::Run::EMBOSSacd - class for EMBOSS Application qualifiers use Bio::Factory::EMBOSS; # get an EMBOSS application object from the EMBOSS factory $factory = new Bio::Factory::EMBOSS $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 # (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 } 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.

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 the web: http://bugzilla.bioperl.org/ Email: heikki@ebi.ac.uk 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 _

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