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 which primes it by reading in the ADC description of the command line options. See also Bio::Factory::EMBOSS.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
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
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
Do not call these methods directly
Title : _acd2input Usage : $embossfactory->_acd2input() Function: compares ACD file requirements to input hash Returns : Throws : if requirements are not met Args : None
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.