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)
Check Out this Related Man Page
Bio::Tools::Run::EMBOSSApplication(3pm) User Contributed Perl Documentation Bio::Tools::Run::EMBOSSApplication(3pm) NAME
Bio::Tools::Run::EMBOSSApplication - class for EMBOSS Applications SYNOPSIS
use Bio::Factory::EMBOSS; # get an EMBOSS application object from the EMBOSS factory $factory = Bio::Factory::EMBOSS->new(); $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 . " "; $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 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 = Bio::AlignIO->new(-format => 'emboss', -file => $wateroutfile); while ( my $aln = $alnin->next_aln ) { # process the alignment -- these will be Bio::SimpleAlign objects } DESCRIPTION
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. 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 CONTRIBUTORS Email: jason-AT-bioperl_DOT_org APPENDIX
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 program_dir Title : program_dir Usage : Function: Required by WrapperBase Throws : Returns : Name of directory with EMBOSS programs Args : program_path Title : program_path Usage : Function: Required by WrapperBase Throws : Returns : Full path of program Args : executable Title : executable Usage : Function: Required by WrapperBase Throws : Returns : Name of program Args : perl v5.12.3 2011-06-18 Bio::Tools::Run::EMBOSSApplication(3pm)