Bio::Factory::EMBOSS - EMBOSS appliaction factory class # 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'); # 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 EMBOSS factory class encapsulates access to EMBOSS programs. A factory object allows creation of only known applications. If you want to check command line options before sending them to the program set $factory->verbose to positive integer. The value is passed on to programs objects and the ADC description of the available command line options is parsed and compared to input. See also Bio::Tools::Run::EMBOSSApplication and Bio::Tools::Run::EMBOSSacd.

Mailing Lists
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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 _

location
Title : location Usage : $embossfactory->location Function: get/set the location of EMBOSS programs. Valid values are 'local' and 'novella'. Returns : string, defaults to 'local' Args : string

program
Title : program Usage : $embossfactory->program('program_name') Function: Creates a representation of a single EMBOSS program Returns : Bio::Tools::Run::EMBOSSApplication object Args : string, program name

version
Title : $self->version Usage : $embossfactory->version() Function: gets the version of EMBOSS programs Throws : if EMBOSS suite is not accessible Returns : version value Args : None

Programs
These methods allow the programmer to query the EMBOSS suite and find out which program names can be used and what arguments can be used.

program_info
Title : program_info Usage : $embossfactory->program_info('emma') Function: Finds out if the program is available. Returns : definition string of the program, undef if program name not known Args : string, prgramname

Internal methods
Do not call these methods directly

_program_list
Title : _program_list Usage : $embossfactory->_program_list() Function: Finds out what programs are available. Writes the names into an internal hash. Returns : true if successful Args : None