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# $Id: satellites.pm,v 1.6 2006/07/04 22:23:35 mauricio Exp $
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# BioPerl module for Bio::Tools::Run::PiseApplication::satellites
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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::satellites
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Bio::Tools::Run::PiseApplication::satellites
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satellites identifying satellites and periodic repetitions in biological sequence s (constrained version) (MF. Sagot, G. Myers, E. Poiret)
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http://bioweb.pasteur.fr/seqanal/interfaces/satellites.html
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for available values):
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Alphabets and score system (-a)
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Minimum length of repeats (minlen)
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Maximum length of repeats (maxlen)
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Maximum number of errors allowed between each repeat and the model for a satellite (not more than 10% of the model length) (maxerr)
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Insertions and deletions allowed (indel)
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Maximum number of 'bad' repeats between 2 'good' ones (not more than 5) (maxjump)
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Minimum number of repeats a satellite must have (quorum)
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Use scores instead of matrix (usematrix)
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Score attributed to a match for the final scoring of a model (scorematch)
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Score attributed to a substitution for the final scoring of a model (scoresub)
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Score attributed to an indel for the final scoring of a model (scoregap)
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Filter threshold (threshold)
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Print threshold (i.e minimum score for printing a model) (threscore)
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Inverted occurences allowed (inverted)
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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/satellites.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::satellites;
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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 $satellites = Bio::Tools::Run::PiseApplication::satellites->new($location, $email, @params);
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Function: Creates a Bio::Tools::Run::PiseApplication::satellites 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 $satellites = $factory->program('satellites');
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Returns : An instance of Bio::Tools::Run::PiseApplication::satellites.
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my ($class, $location, $email, @params) = @_;
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my $self = $class->SUPER::new($location, $email);
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# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/satellites.pm
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$self->{COMMAND} = "satellites";
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$self->{VERSION} = "5.a";
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$self->{TITLE} = "satellites";
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$self->{DESCRIPTION} = "identifying satellites and periodic repetitions in biological sequence s (constrained version)";
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$self->{OPT_EMAIL} = 0;
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$self->{AUTHORS} = "MF. Sagot, G. Myers, E. Poiret";
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$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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"seq", # Sequence File
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"alphabet", # Alphabets and score system (-a)
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"minlen", # Minimum length of repeats (minlen)
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"maxlen", # Maximum length of repeats (maxlen)
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"maxerr", # Maximum number of errors allowed between each repeat and the model for a satellite (not more than 10% of the model length) (maxerr)
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"indel", # Insertions and deletions allowed (indel)
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"maxjump", # Maximum number of 'bad' repeats between 2 'good' ones (not more than 5) (maxjump)
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"quorum", # Minimum number of repeats a satellite must have (quorum)
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"usematrix", # Use scores instead of matrix (usematrix)
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"scorematch", # Score attributed to a match for the final scoring of a model (scorematch)
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"scoresub", # Score attributed to a substitution for the final scoring of a model (scoresub)
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"scoregap", # Score attributed to an indel for the final scoring of a model (scoregap)
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"threshold", # Filter threshold (threshold)
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"threscore", # Print threshold (i.e minimum score for printing a model) (threscore)
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"inverted", # Inverted occurences allowed (inverted)
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"xml", # XML output (xml)
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"satellites" => 'String',
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"param" => 'Results',
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"alphabet" => 'Excl',
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"outputbase" => 'String',
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"scoreN" => 'String',
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"maxsym" => 'String',
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"resultsfiles" => 'Results',
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"minlen" => 'Integer',
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"maxlen" => 'Integer',
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"maxerr" => 'Integer',
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"maxjump" => 'Integer',
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"quorum" => 'Integer',
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"usematrix" => 'Switch',
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"scorematch" => 'Integer',
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"scoresub" => 'Integer',
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"scoregap" => 'Integer',
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"threshold" => 'Integer',
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"threscore" => 'Integer',
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"inverted" => 'Switch',
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"ngroup" => 'String',
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"xmldtdcopy" => 'String',
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"dtdfile" => 'Results',
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"perl" => ' "sat -p params" ',
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"perl" => '" -f $value"',
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"perl" => '" -a /local/gensoft/lib/satellites/alphabets/$value"',
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"perl" => ' "outputbase: results\\n" ',
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"perl" => ' "scoreN: 0\\n" ',
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"perl" => ' "maxsym: 0\\n" ',
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"perl" => ' "minrange: $minlen\\nmaxrange: $maxlen\\n" ',
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"perl" => '"gap: $maxerr\\n"',
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"perl" => '"minlen: $value\\n"',
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"perl" => '"maxlen: $value\\n"',
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"perl" => '"maxerr: $value\\n"',
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"perl" => '($value)? "indel: 1\\n" : "indel: 0\\n" ',
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"perl" => '"maxjump: $value\\n"',
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"perl" => '"quorum: $value\\n"',
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"perl" => '($value)? "usematrix: 0\\n" : "usematrix: 1\\n"',
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"perl" => '"scorematch: $value\\n"',
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"perl" => '"scoresub: $value\\n"',
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"perl" => '"scoregap: $value\\n"',
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"perl" => '"threshold: $value\\n"',
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"perl" => '"threscore: $value\\n"',
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"perl" => '($value)? "inverted: 1\\n" : "inverted: 0\\n" ',
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"perl" => ' "ngroup: 27\\n1 A\\n2 B\\n3 C\\n4 D\\n5 E\\n6 F\\n7 G\\n8 H\\n9 I\\n10 J\\n11 K\\n12 L\\n13 M\\n14 N\\n15 O\\n16 P\\n17 Q\\n18 R\\n19 S\\n20 T\\n21 U\\n22 V\\n23 W\\n24 X\\n25 Y\\n26 Z\\n27 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z\\n" ',
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"perl" => '($value)? "xml: 1\\n" : "" ',
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"perl" => '"; cp /local/gensoft/lib/satellites/satellites.dtd ."',
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$self->{FILENAMES} = {
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"resultsfiles" => 'results*',
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"dtdfile" => 'satellites.dtd',
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$self->{BY_GROUP_PARAMETERS} = [
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$self->{ISHIDDEN} = {
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$self->{ISCOMMAND} = {
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$self->{ISMANDATORY} = {
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"seq" => "Sequence File",
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"alphabet" => "Alphabets and score system (-a)",
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"resultsfiles" => "",
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"minlen" => "Minimum length of repeats (minlen)",
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"maxlen" => "Maximum length of repeats (maxlen)",
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"maxerr" => "Maximum number of errors allowed between each repeat and the model for a satellite (not more than 10% of the model length) (maxerr)",
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"indel" => "Insertions and deletions allowed (indel)",
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"maxjump" => "Maximum number of 'bad' repeats between 2 'good' ones (not more than 5) (maxjump)",
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"quorum" => "Minimum number of repeats a satellite must have (quorum)",
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"usematrix" => "Use scores instead of matrix (usematrix)",
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"scorematch" => "Score attributed to a match for the final scoring of a model (scorematch)",
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"scoresub" => "Score attributed to a substitution for the final scoring of a model (scoresub)",
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"scoregap" => "Score attributed to an indel for the final scoring of a model (scoregap)",
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"threshold" => "Filter threshold (threshold)",
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"threscore" => "Print threshold (i.e minimum score for printing a model) (threscore)",
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"inverted" => "Inverted occurences allowed (inverted)",
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"xml" => "XML output (xml)",
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$self->{ISSTANDOUT} = {
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"alphabet" => ['dna.alphab','DNA','prot.alphab','protein identity','blosum62.alphab','blosum62','pam250.alphab','pam250',],
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$self->{SEPARATOR} = {
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"alphabet" => 'dna.alphab',
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"threshold" => '800',
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"satellites" => { "perl" => '1' },
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"param" => { "perl" => '1' },
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"seq" => { "perl" => '1' },
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"alphabet" => { "perl" => '1' },
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"outputbase" => { "perl" => '1' },
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"scoreN" => { "perl" => '1' },
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"maxsym" => { "perl" => '1' },
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"resultsfiles" => { "perl" => '1' },
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"range" => { "perl" => '1' },
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"gap" => { "perl" => '1' },
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"minlen" => { "perl" => '1' },
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"maxlen" => { "perl" => '1' },
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"maxerr" => { "perl" => '1' },
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"indel" => { "perl" => '1' },
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"maxjump" => { "perl" => '1' },
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"quorum" => { "perl" => '1' },
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"usematrix" => { "perl" => '1' },
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"scorematch" => { "perl" => '1' },
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"scoresub" => { "perl" => '1' },
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"scoregap" => { "perl" => '1' },
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"threshold" => { "perl" => '1' },
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"threscore" => { "perl" => '1' },
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"inverted" => { "perl" => '1' },
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"ngroup" => { "perl" => '1' },
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"xml" => { "perl" => '1' },
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'$maxlen > 50' => "Maximum value : 50",
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'($maxlen > 10 && $maxerr > (($maxlen / 100) * 10)) || ($maxlen <= 10 && $maxerr > 1)' => "The number of errors may not be more than 10% of the model length",
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'$maxjump > 5' => "The number of 'bad' repeats may not be more than 5",
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'$value < 0' => "please enter a non-negative integer value",
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$self->{WITHPIPEOUT} = {
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$self->{WITHPIPEIN} = {
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$self->{ISSIMPLE} = {
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$self->{PARAMFILE} = {
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"outputbase" => "params",
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"scoreN" => "params",
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"maxsym" => "params",
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"minlen" => "params",
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"maxlen" => "params",
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"maxerr" => "params",
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"maxjump" => "params",
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"quorum" => "params",
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"usematrix" => "params",
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"scorematch" => "params",
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"scoresub" => "params",
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"scoregap" => "params",
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"threshold" => "params",
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"threscore" => "params",
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"inverted" => "params",
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"ngroup" => "params",
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"i.e having more than the maximum number of errors allowed",
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"Corresponds to min_repeat in the paper",
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"If unset, will use the score matrix, otherwise will use scorematch and scoresub.",
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"Set it to 0 for guaranteed exhaustive search.",
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"Suggestion: set it to 800 for 10%-15% error rate.",
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"Suggestion: for a flexible search, if the scoring values are the ones suggested, set it to 50.",
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"For a more pertinent search, set it to 100.",
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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/satellites.pm
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$self->_init_params(@params);
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1; # Needed to keep compiler happy
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removed
Bio/Tools/Run/PiseApplication/satellites.pm
