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.IX Title "Bio::Factory::EMBOSS 3pm"
.TH Bio::Factory::EMBOSS 3pm 2024-03-12 "perl v5.38.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH NAME
Bio::Factory::EMBOSS \- EMBOSS application factory class
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 5
\&  # Get an EMBOSS factory
\&  use Bio::Factory::EMBOSS;
\&  $f = Bio::Factory::EMBOSS \-> new();
\&  # Get an EMBOSS application  object from the factory
\&  $water = $f\->program(\*(Aqwater\*(Aq) || die "Program not found!\en";
\&
\&  # 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 = \*(Aqout.water\*(Aq;
\&  $water\->run({\-asequence => $seq_object,
\&               \-bsequence => \e@seq_objects,
\&               \-gapopen   => \*(Aq10.0\*(Aq,
\&               \-gapextend => \*(Aq0.5\*(Aq,
\&               \-outfile   => $wateroutfile});
\&
\&  # Now you might want to get the alignment
\&  use Bio::AlignIO;
\&  my $alnin = Bio::AlignIO\->new(\-format => \*(Aqemboss\*(Aq,
\&                                \-file   => $wateroutfile);
\&
\&  while ( my $aln = $alnin\->next_aln ) {
\&      # process the alignment \-\- these will be Bio::SimpleAlign objects
\&  }
.Ve
.SH DESCRIPTION
.IX Header "DESCRIPTION"
The EMBOSS factory class encapsulates access to EMBOSS programs.  A
factory object allows creation of only known applications.
.PP
If you want to check command line options before sending them to the
program set \f(CW$prog\fR\->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.
.PP
See also Bio::Tools::Run::EMBOSSApplication and
Bio::Tools::Run::EMBOSSacd.
.SH FEEDBACK
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS Support
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Heikki Lehvaslaiho"
.IX Header "AUTHOR - Heikki Lehvaslaiho"
Email heikki-at-bioperl-dot-org
.SH APPENDIX
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS location
.IX Subsection "location"
.Vb 6
\& Title   : location
\& Usage   : $embossfactory\->location
\& Function: get/set the location of EMBOSS programs.
\&           Valid values are \*(Aqlocal\*(Aq and \*(Aqnovella\*(Aq.
\& Returns : string, defaults to \*(Aqlocal\*(Aq
\& Args    : string
.Ve
.SS program
.IX Subsection "program"
.Vb 6
\& Title   : program
\& Usage   : $embossfactory\->program(\*(Aqprogram_name\*(Aq)
\& Function: Creates a representation of a single EMBOSS program and issues a
\&           warning if the program was not found.
\& Returns : Bio::Tools::Run::EMBOSSApplication object or undef
\& Args    : string, program name
.Ve
.SS version
.IX Subsection "version"
.Vb 6
\& 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
.Ve
.SS Programs
.IX Subsection "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.
.SS program_info
.IX Subsection "program_info"
.Vb 5
\& Title   : program_info
\& Usage   : $embossfactory\->program_info(\*(Aqemma\*(Aq)
\& Function: Finds out if the program is available.
\& Returns : definition string of the program, undef if program name not known
\& Args    : string, prgramname
.Ve
.SS "Internal methods"
.IX Subsection "Internal methods"
Do not call these methods directly
.SS _program_list
.IX Subsection "_program_list"
.Vb 6
\& 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
.Ve