Bio::Tools::Run::EMBOSSApplication - class for EMBOSS Applications 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 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.

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CONTRIBUTORS
Email: jason@bioperl.org 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