# $Id: stssearch.pm,v 1.3 2003/06/14 06:05:24 letondal Exp $ # BioPerl module for Bio::Tools::Run::PiseApplication::stssearch # # Cared for by Catherine Letondal # # For copyright and disclaimer see below. # # POD documentation - main docs before the code =head1 NAME Bio::Tools::Run::PiseApplication::stssearch =head1 SYNOPSIS # =head1 DESCRIPTION Bio::Tools::Run::PiseApplication::stssearch Bioperl class for: STSSEARCH Searches a DNA database for matches with a set of STS primers (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/stssearch.html for available values): stssearch (String) init (String) sequences (Sequence) sequences -- dna [sequences] (-sequences) pipe: seqsfile primers (InFile) Primer file (-primers) out (OutFile) out (-out) auto (String) =head1 FEEDBACK =head2 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 list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bioperl.org http://bioperl.org/bioperl-bugs/ =head1 AUTHOR Catherine Letondal (letondal@pasteur.fr) =head1 COPYRIGHT Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 SEE ALSO =over =item * http://bioweb.pasteur.fr/seqanal/interfaces/stssearch.html =item * Bio::Tools::Run::PiseApplication =item * Bio::Tools::Run::AnalysisFactory::Pise =item * Bio::Tools::Run::PiseJob =back =cut #' package Bio::Tools::Run::PiseApplication::stssearch; use vars qw(@ISA); use strict; use Bio::Tools::Run::PiseApplication; @ISA = qw(Bio::Tools::Run::PiseApplication); =head2 new Title : new() Usage : my $stssearch = Bio::Tools::Run::PiseApplication::stssearch->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::stssearch object. This method should not be used directly, but rather by a Bio::Tools::Run::AnalysisFactory::Pise instance. my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new(); my $stssearch = $factory->program('stssearch'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::stssearch. =cut sub new { my ($class, $location, $email, @params) = @_; my $self = $class->SUPER::new($location, $email); # -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/stssearch.pm $self->{COMMAND} = "stssearch"; $self->{VERSION} = "5.a"; $self->{TITLE} = "STSSEARCH"; $self->{DESCRIPTION} = "Searches a DNA database for matches with a set of STS primers (EMBOSS)"; $self->{OPT_EMAIL} = 0; $self->{CATEGORIES} = [ "nucleic:primers", ]; $self->{DOCLINK} = "http://www.uk.embnet.org/Software/EMBOSS/Apps/stssearch.html"; $self->{_INTERFACE_STANDOUT} = undef; $self->{_STANDOUT_FILE} = undef; $self->{TOP_PARAMETERS} = [ "stssearch", "init", "input", "output", "auto", ]; $self->{PARAMETERS_ORDER} = [ "stssearch", "init", "input", # input Section "sequences", # sequences -- dna [sequences] (-sequences) "primers", # Primer file (-primers) "output", # output Section "out", # out (-out) "auto", ]; $self->{TYPE} = { "stssearch" => 'String', "init" => 'String', "input" => 'Paragraph', "sequences" => 'Sequence', "primers" => 'InFile', "output" => 'Paragraph', "out" => 'OutFile', "auto" => 'String', }; $self->{FORMAT} = { "init" => { "perl" => ' "" ', }, "input" => { }, "sequences" => { "perl" => '" -sequences=$value -sformat=fasta"', }, "primers" => { "perl" => '" -primers=$value"', }, "output" => { }, "out" => { "perl" => '" -out=$value"', }, "auto" => { "perl" => '" -auto -stdout"', }, "stssearch" => { "perl" => '"stssearch"', } }; $self->{FILENAMES} = { }; $self->{SEQFMT} = { "sequences" => [8], }; $self->{GROUP} = { "init" => -10, "sequences" => 1, "primers" => 2, "out" => 3, "auto" => 4, "stssearch" => 0 }; $self->{BY_GROUP_PARAMETERS} = [ "init", "input", "output", "stssearch", "sequences", "primers", "out", "auto", ]; $self->{SIZE} = { }; $self->{ISHIDDEN} = { "init" => 1, "input" => 0, "sequences" => 0, "primers" => 0, "output" => 0, "out" => 0, "auto" => 1, "stssearch" => 1 }; $self->{ISCOMMAND} = { "init" => 0, "input" => 0, "sequences" => 0, "primers" => 0, "output" => 0, "out" => 0, "auto" => 0, }; $self->{ISMANDATORY} = { "init" => 0, "input" => 0, "sequences" => 1, "primers" => 1, "output" => 0, "out" => 1, "auto" => 0, }; $self->{PROMPT} = { "init" => "", "input" => "input Section", "sequences" => "sequences -- dna [sequences] (-sequences)", "primers" => "Primer file (-primers)", "output" => "output Section", "out" => "out (-out)", "auto" => "", }; $self->{ISSTANDOUT} = { "init" => 0, "input" => 0, "sequences" => 0, "primers" => 0, "output" => 0, "out" => 0, "auto" => 0, }; $self->{VLIST} = { "input" => ['sequences','primers',], "output" => ['out',], }; $self->{FLIST} = { }; $self->{SEPARATOR} = { }; $self->{VDEF} = { "out" => 'out.out', }; $self->{PRECOND} = { "init" => { "perl" => '1' }, "input" => { "perl" => '1' }, "sequences" => { "perl" => '1' }, "primers" => { "perl" => '1' }, "output" => { "perl" => '1' }, "out" => { "perl" => '1' }, "auto" => { "perl" => '1' }, }; $self->{CTRL} = { }; $self->{PIPEOUT} = { }; $self->{WITHPIPEOUT} = { }; $self->{PIPEIN} = { "sequences" => { "seqsfile" => '1', }, }; $self->{WITHPIPEIN} = { }; $self->{ISCLEAN} = { "init" => 0, "input" => 0, "sequences" => 0, "primers" => 0, "output" => 0, "out" => 0, "auto" => 0, }; $self->{ISSIMPLE} = { "init" => 0, "input" => 0, "sequences" => 1, "primers" => 1, "output" => 0, "out" => 1, "auto" => 0, }; $self->{PARAMFILE} = { }; $self->{COMMENT} = { }; $self->{SCALEMIN} = { }; $self->{SCALEMAX} = { }; $self->{SCALEINC} = { }; $self->{INFO} = { }; # -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/stssearch.pm $self->_init_params(@params); return $self; } 1; # Needed to keep compiler happy