emboss::gui::conf(3pm) [debian man page]
EMBOSS::GUI::Conf(3pm) User Contributed Perl Documentation EMBOSS::GUI::Conf(3pm) NAME
EMBOSS::GUI::Conf - repository for EMBOSS::GUI site-specific configuration AUTHOR
Luke McCarthy <lukem@gene.pbi.nrc.ca> SYNOPSIS
use EMBOSS::GUI::Conf; $conf = EMBOSS::GUI::Conf->new(); foreach $app ($conf->apps) { ($name, $doc) = @$app; if (!$conf->is_excluded($name)) { ... } } foreach $group ($conf->groups) { $group_name = shift @$group; if (!conf->is_excluded($group_name) { foreach $app (@$group) { ($name, $doc) = @$app; ... } } } DESCRIPTION
EMBOSS::GUI::Conf contains site-specific configuration information for EMBOSS::GUI. Consult the source for a description of the variables that can be set. Public methods are described below: new() Returns a new EMBOSS::GUI::Conf object. This method stores the EMBOSS::GUI::Conf package variables in the object hash, ensures that the specified output path is writeable and adds the EMBOSS binaries to the path. apps() Returns a list of available EMBOSS applications. Each element of the list is a reference to an array containing the name and description of an application. groups() Returns a list of application groups. Each element of the list is a reference to an array containing the name of the group and a list of applications belonging to that group (each application is in turn a reference to an array as described in apps() above.) Note that an individual application can appear in multiple groups. is_excluded($subject) Returns true if the subject is being excluded from public display, false otherwise. $subject is the name of an application or application group as it appears in the output from wossname. databases() Returns a list of available databases. Each element of the list is the name of a database, suitable for use in a USA. matrices() Returns a list of available alignment scoring matrices. Each element of the list is a reference to an array containing the filename of the scoring matrix, suitable for use as the value of a matrix or matrixf argument, and a description of the matrix. codon_usage_tables() Returns a list of available codon usage tables. Each element of the list is a reference to an array containing the filename of the codon usage table, suitable for use as the value of a codon argument, and the name of the species from which it is derived. 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 2013-09-16 EMBOSS::GUI::Conf(3pm)
Check Out this Related Man Page
Bio::Tools::Run::EMBOSSacd(3pm) User Contributed Perl Documentation Bio::Tools::Run::EMBOSSacd(3pm) NAME
Bio::Tools::Run::EMBOSSacd - class for EMBOSS Application qualifiers 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 # (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 = Bio::AlignIO->new(-format => 'emboss', -file => $wateroutfile); while( my $aln = $alnin->next_aln ) { # process the alignment -- these will be Bio::SimpleAlign objects } DESCRIPTION
The EMBOSSacd represents all the possible command line arguments that can be given to an EMBOSS application. Do not create this object directly. It will be created and attached to its corresponding Bio::Tools::Run::EMBOSSApplication if you set $application->verbose > 0 Call $application->acd to retrive the Bio::Tools::Run::EMBOSSApplication::EMBOSSacd object. See also Bio::Tools::Run::EMBOSSApplication and Bio::Factory::EMBOSS. 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 Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : $emboss_prog->acd($prog_name); Function: Constructor for the class. Calls EMBOSS program 'acdc', converts the HTML output into XML and uses XML::Twig XML parser to write out a hash of qualifiers which is then blessed. Throws : without program name Returns : new object Args : EMBOSS program name name Title : name Usage : $embossacd->name Function: sets/gets the name of the EMBOSS program Setting is done by the EMBOSSApplication object, you should only get it. Throws : Returns : name string Args : None print Title : print Usage : $embossacd->print; $embossacd->print('-word'); Function: Print out the qualifiers. Uses Data::Dumper to print the qualifiers into STDOUT. A valid qualifier name given as an argment limits the output. Throws : Returns : print string Args : optional qualifier name mandatory Title : mandatory Usage : $acd->mandatory Function: gets a mandatory subset of qualifiers Throws : Returns : Bio::Tools::Run::EMBOSSacd object Args : none Qualifier queries These methods can be used test qualifier names and read values. qualifier Title : qualifier Usage : $acd->qualifier($string) Function: tests for the existence of the qualifier Throws : Returns : boolean Args : string, name of the qualifier category Title : category Usage : $acd->category($qual_name) Function: Return the category of the qualifier Throws : Returns : 'mandatory' or 'optional' or 'advanced' or 'associated' or 'general' Args : string, name of the qualifier values Title : values Usage : $acd->values($qual_name) Function: Return the possible values for the qualifier Throws : Returns : string Args : string, name of the qualifier descr Title : descr Usage : $acd->descr($qual_name) Function: Return the description of the qualifier Throws : Returns : boolean Args : string, name of the qualifier unnamed Title : unnamed Usage : $acd->unnamed($qual_name) Function: Find if the qualifier can be left unnamed Throws : Returns : 0 if needs to be named, order number otherwise Args : string, name of the qualifier default Title : default Usage : $acd->default($qual_name) Function: Return the default value for the qualifier Throws : Returns : scalar Args : string, name of the qualifier perl v5.12.3 2011-06-18 Bio::Tools::Run::EMBOSSacd(3pm)