emboss::acd(3pm) [debian man page]
EMBOSS::ACD(3pm) User Contributed Perl Documentation EMBOSS::ACD(3pm) NAME
EMBOSS::ACD - parse EMBOSS ACD (AJAX Command Definition) files AUTHOR
Luke McCarthy <lukem@gene.pbi.nrc.ca> SYNOPSIS
use EMBOSS::ACD; $acd = EMBOSS::ACD->new($acdfile); $application = $acd->name; $description = $acd->documentation; @groups = $acd->groups; foreach $parameter ($acd->param) { while (($attribute, $value) = each %$parameter) { ... } } DESCRIPTION
EMBOSS::ACD parses EMBOSS Ajax Command Definition files and provides object-oriented access to the data contained therein. For a complete specification of the ACD format, see http://emboss.sourceforge.net/developers/acd Note that no checks are performed to ensure that the ACD file is semantically valid. Specifically, datatypes and attributes that aren't defined in the specification can occur in the file and will be parsed as normal. This is a good thing, as the module remains useful even if new datatypes are added by local developers or the EMBOSS crew. Public methods are described below: new($acdfile) Parses the specified ACD file. Returns a new EMBOSS::ACD object on success, and dies on failure. $acdfile is the full path to a valid ACD file. name() Returns the name of the application whose ACD file was parsed. documentation() Returns a short description of the application whose ACD file was parsed. groups() Returns a list of functional groups to which the application belongs. For a list of possible groups, see http://emboss.sourceforge.net/developers/acd/syntax.html#sect2214 param($param) Returns a reference to a hash describing the specified parameter. The hash contains key-value pairs corresponding to the attributes specified in the ACD file, plus the keys 'name' and 'datatype'. The value of the 'datatype' key is the canonical name of the data type, regardless of any abbreviation in the ACD file. For a list of possible data types, see http://emboss.sourceforge.net/developers/acd/syntax.html#sect23 If no parameter is specified, a list of all parameters is returned. The members of the list are hash references as described above. Note that, in accordance with the ACD specification, attribute names are not expanded if they are abbreviated in the ACD file. $param is either undefined (see above) or the name of the desired parameter. canonical_datatype($datatype) Returns the canonical name of the specified abbreviated datatype, or undefined if the abbreviation is ambiguous or not recognized. BUGS
None that I know of... COPYRIGHT
Copyright (c) 2004 Luke McCarthy. All rights reserved. This program is free software. You may copy or redistribute it under the same terms as Perl itself. perl v5.14.2 2005-10-27 EMBOSS::ACD(3pm)
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Bio::Factory::EMBOSS(3pm) User Contributed Perl Documentation Bio::Factory::EMBOSS(3pm) NAME
Bio::Factory::EMBOSS - EMBOSS application factory class SYNOPSIS
# 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 sequence against 1 or more 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({-sequences => $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 = Bio::AlignIO->new(-format => 'emboss', -file => $wateroutfile); while ( my $aln = $alnin->next_aln ) { # process the alignment -- these will be Bio::SimpleAlign objects } DESCRIPTION
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 $prog->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. FEEDBACK
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://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org 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. 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://redmine.open-bio.org/projects/bioperl/ AUTHOR - Heikki Lehvaslaiho Email heikki-at-bioperl-dot-org APPENDIX
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 perl v5.12.3 2011-06-18 Bio::Factory::EMBOSS(3pm)