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# $Id: grailclnt.pm,v 1.8 2006/07/04 22:23:34 mauricio Exp $
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# BioPerl module for Bio::Tools::Run::PiseApplication::grailclnt
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# Cared for by Catherine Letondal <letondal@pasteur.fr>
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# For copyright and disclaimer see below.
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# POD documentation - main docs before the code
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Bio::Tools::Run::PiseApplication::grailclnt
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Bio::Tools::Run::PiseApplication::grailclnt
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GRAILCLNT Grail client (Xu, Einstein, Mural, Shah, Uberbacher)
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Xu, Y., Einstein, J. R., Mural, R.J., Shah, M. and Uberbacher, E.C., (1994) An Improved System for Exon Recognition and Gene Modeling in Human DNA Sequences, Published Presentation: The Second International Conference on Intelligent Systems for Molecular Biology, Stanford University, San Francisco, CA, August 14-17, 1994.
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http://bioweb.pasteur.fr/seqanal/interfaces/grailclnt.html
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for available values):
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Shadowexons (grail 1.a or grail2)
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grail2exons results file
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modelexon_translation (Switch)
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Gene model exons translation
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genemodel_translation (Switch)
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Entire gene models translation
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start_strand (Integer)
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forward_strand (Switch)
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reverse_strand (Switch)
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grail2exons results file
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rpttv_organism (String)
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User feedback is an integral part of the evolution of this and other
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Bioperl modules. Send your comments and suggestions preferably to
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the Bioperl mailing list. Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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=head2 Reporting Bugs
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Report bugs to the Bioperl bug tracking system to help us keep track
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of the bugs and their resolution. Bug reports can be submitted via the
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http://bugzilla.open-bio.org/
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Catherine Letondal (letondal@pasteur.fr)
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Copyright (C) 2003 Institut Pasteur & Catherine Letondal.
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This module is free software; you can redistribute it and/or modify
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it under the same terms as Perl itself.
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This software is provided "as is" without warranty of any kind.
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http://bioweb.pasteur.fr/seqanal/interfaces/grailclnt.html
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Bio::Tools::Run::PiseApplication
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Bio::Tools::Run::AnalysisFactory::Pise
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Bio::Tools::Run::PiseJob
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package Bio::Tools::Run::PiseApplication::grailclnt;
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use Bio::Tools::Run::PiseApplication;
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@ISA = qw(Bio::Tools::Run::PiseApplication);
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Usage : my $grailclnt = Bio::Tools::Run::PiseApplication::grailclnt->new($location, $email, @params);
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Function: Creates a Bio::Tools::Run::PiseApplication::grailclnt object.
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This method should not be used directly, but rather by
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a Bio::Tools::Run::AnalysisFactory::Pise instance.
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my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
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my $grailclnt = $factory->program('grailclnt');
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Returns : An instance of Bio::Tools::Run::PiseApplication::grailclnt.
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my ($class, $location, $email, @params) = @_;
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my $self = $class->SUPER::new($location, $email);
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# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/grailclnt.pm
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$self->{COMMAND} = "grailclnt";
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$self->{VERSION} = "5.a";
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$self->{TITLE} = "GRAILCLNT";
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$self->{DESCRIPTION} = "Grail client";
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$self->{OPT_EMAIL} = 0;
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$self->{AUTHORS} = "Xu, Einstein, Mural, Shah, Uberbacher";
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$self->{REFERENCE} = [
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"Xu, Y., Einstein, J. R., Mural, R.J., Shah, M. and Uberbacher, E.C., (1994) An Improved System for Exon Recognition and Gene Modeling in Human DNA Sequences, Published Presentation: The Second International Conference on Intelligent Systems for Molecular Biology, Stanford University, San Francisco, CA, August 14-17, 1994.",
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$self->{_INTERFACE_STANDOUT} = undef;
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$self->{_STANDOUT_FILE} = undef;
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$self->{TOP_PARAMETERS} = [
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$self->{PARAMETERS_ORDER} = [
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"feature", # Which feature?
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"organism", # Organism
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"exons_options", # Exons options
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"translation", # Translation
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"strandscores", # Strandscores (grail1)
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"shadowexons", # Shadowexons (grail 1.a or grail2)
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"clusters", # Clusters (grail 2)
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"gap_options", # Gene modelling options
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"cluster_file", # grail2exons results file
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"modelexon_translation", # Gene model exons translation
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"genemodel_translation", # Entire gene models translation
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"auto_strand", # AUTO STRAND
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"start_strand", # AUTO STRAND start
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"end_strand", # AUTO STRAND end
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"forward_strand", # FORWARD_STRAND
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"reverse_strand", # REVERSE_STRAND
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"polIIprom_options", # Pol II Promoters options
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"grail2_file", # grail2exons results file
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"fserr_options", # fserr options
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"fserr_strand", # Strand
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"outfile", # Result file
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"grailclnt" => 'String',
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"organism" => 'Excl',
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"header" => 'Switch',
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"exons_options" => 'Paragraph',
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"translation" => 'Switch',
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"strandscores" => 'Switch',
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"shadowexons" => 'Switch',
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"clusters" => 'Switch',
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"gap_options" => 'Paragraph',
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"cluster_file" => 'InFile',
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"modelexon_translation" => 'Switch',
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"genemodel_translation" => 'Switch',
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"auto_strand" => 'Switch',
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"start_strand" => 'Integer',
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"end_strand" => 'Integer',
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"forward_strand" => 'Switch',
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"reverse_strand" => 'Switch',
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"polIIprom_options" => 'Paragraph',
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"grail2_file" => 'InFile',
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"fserr_options" => 'Paragraph',
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"fserr_strand" => 'Excl',
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"rpttv_organism" => 'String',
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"start_seq" => 'String',
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"end_seq" => 'String',
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"end_request" => 'String',
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"input_file" => 'Results',
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"outfile" => 'OutFile',
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"perl" => '"cat grail_input_* > grail_input; grailclnt -host grailsrv.lsd.ornl.gov -port 2050 < grail_input " ',
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"perl" => '" ln -s $seq grail_input_a4 ;"',
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"perl" => '($value eq "cpg" || $value eq "rpttv" || $value eq "smprpt")? "\\n\\[Request\\_$value\\_1.3\\]\\n\\n" : "\\n\\[Request\\_$value\\_$organism\\_1.3\\]\\n\\n" ',
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"perl" => '($value)? "[Option= header]\\n" : ""',
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"perl" => '($value)? "[Option= translation]\\n" : ""',
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"perl" => '($value)? "[Option= strandscores]\\n" : ""',
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"perl" => '($value)? "[Option= shadowexons]\\n" : ""',
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"perl" => '($value)? "[Option= clusters]\\n" : ""',
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"perl" => '($value)? "sed -n \\"/^.Start clusters/,/^.End clusters/p\\" $cluster_file > grail_input_b4 ;" : "" ',
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"modelexon_translation" => {
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"perl" => '($value)? "[Option= modelexon_translation]\\n" : ""',
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"genemodel_translation" => {
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"perl" => '($value)? "[Option= genemodel_translation]\\n" : ""',
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"perl" => '($value)? "[Params= AUTO_STRAND $start_strand $end_strand]\\n" : ""',
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"forward_strand" => {
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"perl" => '($value)? "[Params= FORWARD_STRAND]\\n" : ""',
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"reverse_strand" => {
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"perl" => '($value)? "[Params= REVERSE_STRAND]\\n" : ""',
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"polIIprom_options" => {
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"perl" => '($value)? " ln -s $grail2_file grail_input_b2 ;" : "" ',
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"perl" => '"[Params= $value]\\n" ',
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"rpttv_organism" => {
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"perl" => '"\\n\\n[Params= $organism]\\n\\n"',
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"perl" => '"\\n\\n[Start DNASequence]\\n\\n"',
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"perl" => '"\\n\\n[End DNASequence]\\n\\n"',
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"perl" => '"\\n\\n[End_Request]\\n\\n"',
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"perl" => '($value)? " > $value" : ""',
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$self->{FILENAMES} = {
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"input_file" => 'grail_input',
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"modelexon_translation" => 3,
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"genemodel_translation" => 3,
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"forward_strand" => 4,
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"reverse_strand" => 4,
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"rpttv_organism" => 4,
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$self->{BY_GROUP_PARAMETERS} = [
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"modelexon_translation",
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"genemodel_translation",
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$self->{ISHIDDEN} = {
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"exons_options" => 0,
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"modelexon_translation" => 0,
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"genemodel_translation" => 0,
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"forward_strand" => 0,
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"reverse_strand" => 0,
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"polIIprom_options" => 0,
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"fserr_options" => 0,
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"rpttv_organism" => 1,
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$self->{ISCOMMAND} = {
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"exons_options" => 0,
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"modelexon_translation" => 0,
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"genemodel_translation" => 0,
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"forward_strand" => 0,
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"reverse_strand" => 0,
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"polIIprom_options" => 0,
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"fserr_options" => 0,
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"rpttv_organism" => 0,
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$self->{ISMANDATORY} = {
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"exons_options" => 0,
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"modelexon_translation" => 0,
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"genemodel_translation" => 0,
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"forward_strand" => 0,
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"reverse_strand" => 0,
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"polIIprom_options" => 0,
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"fserr_options" => 0,
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"rpttv_organism" => 0,
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"feature" => "Which feature?",
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"organism" => "Organism",
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"header" => "Header",
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"exons_options" => "Exons options",
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"translation" => "Translation",
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"strandscores" => "Strandscores (grail1)",
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"shadowexons" => "Shadowexons (grail 1.a or grail2)",
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"clusters" => "Clusters (grail 2)",
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"gap_options" => "Gene modelling options",
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"cluster_file" => "grail2exons results file",
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"modelexon_translation" => "Gene model exons translation",
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"genemodel_translation" => "Entire gene models translation",
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"auto_strand" => "AUTO STRAND",
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"start_strand" => "AUTO STRAND start",
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"end_strand" => "AUTO STRAND end",
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"forward_strand" => "FORWARD_STRAND",
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"reverse_strand" => "REVERSE_STRAND",
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"polIIprom_options" => "Pol II Promoters options",
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"grail2_file" => "grail2exons results file",
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"fserr_options" => "fserr options",
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"fserr_strand" => "Strand",
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"rpttv_organism" => "",
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"outfile" => "Result file",
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$self->{ISSTANDOUT} = {
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"exons_options" => 0,
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"modelexon_translation" => 0,
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"genemodel_translation" => 0,
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"forward_strand" => 0,
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"reverse_strand" => 0,
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"polIIprom_options" => 0,
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"fserr_options" => 0,
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"rpttv_organism" => 0,
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"feature" => ['grail1exons','grail1exons: Protein Coding Regions (grail 1)','grail1aexons','grail1aexons: Protein Coding Regions (grail 1.a)','grail2exons','grail2exons: Protein Coding Regions (grail 2)','gap2','gap2: Gene Modeling','polya','polya: PolyA sites','polIIprom','polIIprom: Pol II Promoters','cpg','cpg: CpG Islands','rpttv','rpttv: repetitive DNA elements','smprpt','smprpt: simple repeats','fserr','fserr: Frame Shift Errors',],
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"organism" => ['human','Human','mouse','Mouse','arabd','Arabidopsis','droso','Drosophila','ecoli','E. coli',],
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"exons_options" => ['translation','strandscores','shadowexons','clusters',],
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"gap_options" => ['cluster_file','modelexon_translation','genemodel_translation','auto_strand','start_strand','end_strand','forward_strand','reverse_strand',],
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"polIIprom_options" => ['grail2_file',],
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"fserr_options" => ['fserr_strand',],
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"fserr_strand" => ['AUTO_STRAND','AUTO_STRAND','FORWARD_STRAND','FORWARD_STRAND','REVERSE_STRAND','REVERSE_STRAND',],
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$self->{SEPARATOR} = {
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"feature" => 'grail2exons',
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"organism" => 'human',
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"translation" => '0',
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"strandscores" => '0',
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"shadowexons" => '1',
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"modelexon_translation" => '0',
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"genemodel_translation" => '0',
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"auto_strand" => '1',
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"forward_strand" => '0',
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"reverse_strand" => '0',
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"fserr_strand" => 'AUTO_STRAND',
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"outfile" => 'grailclnt.txt',
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"grailclnt" => { "perl" => '1' },
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"seq" => { "perl" => '1' },
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"feature" => { "perl" => '1' },
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"organism" => { "perl" => '1' },
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"header" => { "perl" => '1' },
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"perl" => '$feature =~ /grail/',
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"perl" => '$feature =~ /grail/',
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"perl" => '$feature =~ /grail/ && $feature eq "grail1exons" ',
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"perl" => '$feature =~ /grail/ && $feature ne "grail1exons" ',
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"perl" => '$feature =~ /grail/ && $feature eq "grail2exons" ',
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"perl" => '$feature eq "gap2" ',
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"perl" => '$feature eq "gap2" ',
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"modelexon_translation" => {
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"perl" => '$feature eq "gap2" ',
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"genemodel_translation" => {
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"perl" => '$feature eq "gap2" ',
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"perl" => '$feature eq "gap2" ',
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"perl" => '$feature eq "gap2" && $auto_strand',
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"perl" => '$feature eq "gap2" && $auto_strand',
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"forward_strand" => {
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"perl" => '$feature eq "gap2" && ! $auto_strand',
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"reverse_strand" => {
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"perl" => '$feature eq "gap2" && ! $auto_strand',
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"polIIprom_options" => {
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"perl" => '$feature eq "polIIprom" ',
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"perl" => '$feature eq "polIIprom" ',
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"perl" => '$feature eq "fserr" ',
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"perl" => '$feature eq "fserr" ',
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"rpttv_organism" => {
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"perl" => '$feature eq "rpttv" ',
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"start_seq" => { "perl" => '1' },
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"end_seq" => { "perl" => '1' },
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"end_request" => { "perl" => '1' },
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"input_file" => { "perl" => '1' },
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"outfile" => { "perl" => '1' },
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'$organism eq "ecoli" && (! ($feature eq "grail1" || $feature eq "smprpt")) ' => "E. coli is available only for grail1 or simple repeats",
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'$feature eq "polIIprom" && (! ($organism eq "human" || $organism eq "mouse"))' => "polIIprom is available only for Human or Mouse",
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'$feature eq "rpttv" && (! ($organism eq "human" || $organism eq "mouse"))' => "Repetitive DNA is available only for Human or Mouse",
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'$organism eq "droso" && ($feature =~ /grail1/)' => "Grail 1 or 1.a is not available for drosophila",
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'$feature eq "fserr" && (! ($organism eq "human" || $organism eq "mouse"))' => "fserr is available only for Human or Mouse",
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'$feature eq "polya" && (! ($organism eq "human" || $organism eq "mouse"))' => "polya is available only for Human or Mouse",
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'$organism eq "arabd" && ($feature =~ /grail1/)' => "Grail 1 or 1.a is not available for arabidopsis",
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'$feature eq "cpg" && (! ($organism eq "human" || $organism eq "mouse"))' => "CpG is available only for Human or Mouse",
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'$feature eq "grail2exons" ' => "grail_cluster",
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$self->{WITHPIPEOUT} = {
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"grail_cluster" => '1',
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"grail_cluster" => '1',
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$self->{WITHPIPEIN} = {
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"exons_options" => 0,
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"modelexon_translation" => 0,
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"genemodel_translation" => 0,
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"forward_strand" => 0,
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"reverse_strand" => 0,
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"polIIprom_options" => 0,
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"fserr_options" => 0,
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"rpttv_organism" => 0,
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$self->{ISSIMPLE} = {
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"exons_options" => 0,
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"modelexon_translation" => 0,
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"genemodel_translation" => 0,
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"forward_strand" => 0,
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"reverse_strand" => 0,
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"polIIprom_options" => 0,
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"fserr_options" => 0,
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"rpttv_organism" => 0,
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$self->{PARAMFILE} = {
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"feature" => "grail_input_a1",
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"header" => "grail_input_a1",
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"translation" => "grail_input_a1",
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"strandscores" => "grail_input_a1",
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"shadowexons" => "grail_input_a1",
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"clusters" => "grail_input_a1",
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"modelexon_translation" => "grail_input_a1",
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"genemodel_translation" => "grail_input_a1",
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"auto_strand" => "grail_input_a1",
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"start_strand" => "grail_input_a1",
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"end_strand" => "grail_input_a1",
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"forward_strand" => "grail_input_a1",
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"reverse_strand" => "grail_input_a1",
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"fserr_strand" => "grail_input_a1",
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"rpttv_organism" => "grail_input_a1",
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"start_seq" => "grail_input_a3",
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"end_seq" => "grail_input_a5",
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"end_request" => "grail_input_z9",
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"The coding recognition portion of the system uses a neural network which combines a series of coding prediction algorithms. There are three basic versions of this neural network, GRAIL 1, GRAIL 1a and GRAIL 2: ",
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"GRAIL 1 has been in place for about five years. It uses a neural network described in PNAS 88, 11261-11265, which recognizes coding potential within a fixed size (100 base) window. It evaluates coding potential without looking for additional features (information such as splice junctions, etc).",
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"GRAIL 1a is an updated version of GRAIL 1. It uses a fixed-length window to locate the potential coding regions and then evaluates a number of discrete candidates of different lengths around each potential coding region, using information from the two 60-base regions adjacent to that coding region, to find the \'best\' boundaries for that coding region.",
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"GRAIL 2 uses variable-length windows tailored to each potential exon candidate, defined as an open reading frame bounded by a pair of start/donor, acceptor/donor or acceptor/stop sites. This scheme facilitates the use of more genomic context information (splice junctions, translation starts, non-coding scores of 60-base regions on either side of a putative exon) in the exon recognition process. GRAIL 2 is therefore not appropriate for sequences without genomic context (when the regions adjacent to an exon are not present).",
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"This feature is needed for a further polIIpromoters analysis.",
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"This feature is needed for a further Gene Modelling analysis with GAP2 or polIIpromoters.",
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"For gap2 (gene assembly) the cluster tables returned by grail2exons must be included.",
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"So what you have to do here is to put your grail2exons results, the program will extract clusters from this data.",
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"For Pol II promoters, all the results of grail2 must be included.",
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"The [Start/end header] lines must be removed.",
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$self->{SCALEMIN} = {
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$self->{SCALEMAX} = {
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$self->{SCALEINC} = {
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# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/grailclnt.pm
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$self->_init_params(@params);
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1; # Needed to keep compiler happy
added
removed
Bio/Tools/Run/PiseApplication/grailclnt.pm
