# compseq.pm,v 1.3.2.1 2005/10/09 15:19:44 jason Exp
# BioPerl module for Bio::Tools::Run::PiseApplication::compseq
#
# Cared for by Catherine Letondal <letondal@pasteur.fr>
#
# For copyright and disclaimer see below.
#
# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Run::PiseApplication::compseq

=head1 SYNOPSIS

  #

=head1 DESCRIPTION

Bio::Tools::Run::PiseApplication::compseq

      Bioperl class for:

	COMPSEQ	Counts the composition of dimer/trimer/etc words in a sequence (EMBOSS)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/compseq.html 
         for available values):


		compseq (String)

		init (String)

		sequence (Sequence)
			sequence [sequences] (-sequence)
			pipe: seqsfile

		word (Integer)
			Word size to consider (e.g. 2=dimer) (-word)

		infile (InFile)
			'compseq' file to use for expected word frequencies (-infile)

		frame (Integer)
			Frame of word to look at (0=all frames) (-frame)

		ignorebz (Switch)
			Ignore the amino acids B and Z and just count them as 'Other' (-ignorebz)

		reverse (Switch)
			Count words in the forward and reverse sense (-reverse)

		outfile (OutFile)
			outfile (-outfile)

		zerocount (Switch)
			Display the words that have a frequency of zero (-zerocount)

		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 the
web:

  http://bugzilla.bioperl.org/

=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/compseq.html

=item *

Bio::Tools::Run::PiseApplication

=item *

Bio::Tools::Run::AnalysisFactory::Pise

=item *

Bio::Tools::Run::PiseJob

=back

=cut

#'
package Bio::Tools::Run::PiseApplication::compseq;

use vars qw(@ISA);
use strict;
use Bio::Tools::Run::PiseApplication;

@ISA = qw(Bio::Tools::Run::PiseApplication);

=head2 new

 Title   : new()
 Usage   : my $compseq = Bio::Tools::Run::PiseApplication::compseq->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::compseq 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 $compseq = $factory->program('compseq');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::compseq.

=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/compseq.pm

    $self->{COMMAND}   = "compseq";
    $self->{VERSION}   = "5.a";
    $self->{TITLE}   = "COMPSEQ";

    $self->{DESCRIPTION}   = "Counts the composition of dimer/trimer/etc words in a sequence (EMBOSS)";

    $self->{OPT_EMAIL}   = 0;

    $self->{CATEGORIES}   =  [  

         "nucleic:composition",

         "protein:composition",
  ];

    $self->{DOCLINK}   = "http://www.uk.embnet.org/Software/EMBOSS/Apps/compseq.html";

    $self->{_INTERFACE_STANDOUT} = undef;
    $self->{_STANDOUT_FILE} = undef;

    $self->{TOP_PARAMETERS}  = [ 
	"compseq",
	"init",
	"input",
	"required",
	"advanced",
	"output",
	"auto",

    ];

    $self->{PARAMETERS_ORDER}  = [
	"compseq",
	"init",
	"input", 	# input Section
	"sequence", 	# sequence [sequences] (-sequence)
	"required", 	# required Section
	"word", 	# Word size to consider (e.g. 2=dimer) (-word)
	"advanced", 	# advanced Section
	"infile", 	# 'compseq' file to use for expected word frequencies (-infile)
	"frame", 	# Frame of word to look at (0=all frames) (-frame)
	"ignorebz", 	# Ignore the amino acids B and Z and just count them as 'Other' (-ignorebz)
	"reverse", 	# Count words in the forward and reverse sense (-reverse)
	"output", 	# output Section
	"outfile", 	# outfile (-outfile)
	"zerocount", 	# Display the words that have a frequency of zero (-zerocount)
	"auto",

    ];

    $self->{TYPE}  = {
	"compseq" => 'String',
	"init" => 'String',
	"input" => 'Paragraph',
	"sequence" => 'Sequence',
	"required" => 'Paragraph',
	"word" => 'Integer',
	"advanced" => 'Paragraph',
	"infile" => 'InFile',
	"frame" => 'Integer',
	"ignorebz" => 'Switch',
	"reverse" => 'Switch',
	"output" => 'Paragraph',
	"outfile" => 'OutFile',
	"zerocount" => 'Switch',
	"auto" => 'String',

    };

    $self->{FORMAT}  = {
	"init" => {
		"perl" => ' "" ',
	},
	"input" => {
	},
	"sequence" => {
		"perl" => '" -sequence=$value -sformat=fasta"',
	},
	"required" => {
	},
	"word" => {
		"perl" => '" -word=$value"',
	},
	"advanced" => {
	},
	"infile" => {
		"perl" => '($value)? " -infile=$value" : ""',
	},
	"frame" => {
		"perl" => '(defined $value && $value != $vdef)? " -frame=$value" : ""',
	},
	"ignorebz" => {
		"perl" => '($value)? "" : " -noignorebz"',
	},
	"reverse" => {
		"perl" => '($value)? " -reverse" : ""',
	},
	"output" => {
	},
	"outfile" => {
		"perl" => '" -outfile=$value"',
	},
	"zerocount" => {
		"perl" => '($value)? "" : " -nozerocount"',
	},
	"auto" => {
		"perl" => '" -auto -stdout"',
	},
	"compseq" => {
		"perl" => '"compseq"',
	}

    };

    $self->{FILENAMES}  = {

    };

    $self->{SEQFMT}  = {
	"sequence" => [8],

    };

    $self->{GROUP}  = {
	"init" => -10,
	"sequence" => 1,
	"word" => 2,
	"infile" => 3,
	"frame" => 4,
	"ignorebz" => 5,
	"reverse" => 6,
	"outfile" => 7,
	"zerocount" => 8,
	"auto" => 9,
	"compseq" => 0

    };

    $self->{BY_GROUP_PARAMETERS}  = [
	"init",
	"input",
	"required",
	"advanced",
	"output",
	"compseq",
	"sequence",
	"word",
	"infile",
	"frame",
	"ignorebz",
	"reverse",
	"outfile",
	"zerocount",
	"auto",

    ];

    $self->{SIZE}  = {

    };

    $self->{ISHIDDEN}  = {
	"init" => 1,
	"input" => 0,
	"sequence" => 0,
	"required" => 0,
	"word" => 0,
	"advanced" => 0,
	"infile" => 0,
	"frame" => 0,
	"ignorebz" => 0,
	"reverse" => 0,
	"output" => 0,
	"outfile" => 0,
	"zerocount" => 0,
	"auto" => 1,
	"compseq" => 1

    };

    $self->{ISCOMMAND}  = {
	"init" => 0,
	"input" => 0,
	"sequence" => 0,
	"required" => 0,
	"word" => 0,
	"advanced" => 0,
	"infile" => 0,
	"frame" => 0,
	"ignorebz" => 0,
	"reverse" => 0,
	"output" => 0,
	"outfile" => 0,
	"zerocount" => 0,
	"auto" => 0,

    };

    $self->{ISMANDATORY}  = {
	"init" => 0,
	"input" => 0,
	"sequence" => 1,
	"required" => 0,
	"word" => 1,
	"advanced" => 0,
	"infile" => 0,
	"frame" => 0,
	"ignorebz" => 0,
	"reverse" => 0,
	"output" => 0,
	"outfile" => 1,
	"zerocount" => 0,
	"auto" => 0,

    };

    $self->{PROMPT}  = {
	"init" => "",
	"input" => "input Section",
	"sequence" => "sequence [sequences] (-sequence)",
	"required" => "required Section",
	"word" => "Word size to consider (e.g. 2=dimer) (-word)",
	"advanced" => "advanced Section",
	"infile" => "'compseq' file to use for expected word frequencies (-infile)",
	"frame" => "Frame of word to look at (0=all frames) (-frame)",
	"ignorebz" => "Ignore the amino acids B and Z and just count them as 'Other' (-ignorebz)",
	"reverse" => "Count words in the forward and reverse sense (-reverse)",
	"output" => "output Section",
	"outfile" => "outfile (-outfile)",
	"zerocount" => "Display the words that have a frequency of zero (-zerocount)",
	"auto" => "",

    };

    $self->{ISSTANDOUT}  = {
	"init" => 0,
	"input" => 0,
	"sequence" => 0,
	"required" => 0,
	"word" => 0,
	"advanced" => 0,
	"infile" => 0,
	"frame" => 0,
	"ignorebz" => 0,
	"reverse" => 0,
	"output" => 0,
	"outfile" => 0,
	"zerocount" => 0,
	"auto" => 0,

    };

    $self->{VLIST}  = {

	"input" => ['sequence',],
	"required" => ['word',],
	"advanced" => ['infile','frame','ignorebz','reverse',],
	"output" => ['outfile','zerocount',],
    };

    $self->{FLIST}  = {

    };

    $self->{SEPARATOR}  = {

    };

    $self->{VDEF}  = {
	"word" => '2',
	"frame" => '0',
	"ignorebz" => '1',
	"reverse" => '0',
	"outfile" => 'outfile.out',
	"zerocount" => '1',

    };

    $self->{PRECOND}  = {
	"init" => { "perl" => '1' },
	"input" => { "perl" => '1' },
	"sequence" => { "perl" => '1' },
	"required" => { "perl" => '1' },
	"word" => { "perl" => '1' },
	"advanced" => { "perl" => '1' },
	"infile" => { "perl" => '1' },
	"frame" => { "perl" => '1' },
	"ignorebz" => { "perl" => '1' },
	"reverse" => { "perl" => '1' },
	"output" => { "perl" => '1' },
	"outfile" => { "perl" => '1' },
	"zerocount" => { "perl" => '1' },
	"auto" => { "perl" => '1' },

    };

    $self->{CTRL}  = {

    };

    $self->{PIPEOUT}  = {

    };

    $self->{WITHPIPEOUT}  = {

    };

    $self->{PIPEIN}  = {
	"sequence" => {
		 "seqsfile" => '1',
	},

    };

    $self->{WITHPIPEIN}  = {

    };

    $self->{ISCLEAN}  = {
	"init" => 0,
	"input" => 0,
	"sequence" => 0,
	"required" => 0,
	"word" => 0,
	"advanced" => 0,
	"infile" => 0,
	"frame" => 0,
	"ignorebz" => 0,
	"reverse" => 0,
	"output" => 0,
	"outfile" => 0,
	"zerocount" => 0,
	"auto" => 0,

    };

    $self->{ISSIMPLE}  = {
	"init" => 0,
	"input" => 0,
	"sequence" => 1,
	"required" => 0,
	"word" => 1,
	"advanced" => 0,
	"infile" => 0,
	"frame" => 0,
	"ignorebz" => 0,
	"reverse" => 0,
	"output" => 0,
	"outfile" => 1,
	"zerocount" => 0,
	"auto" => 0,

    };

    $self->{PARAMFILE}  = {

    };

    $self->{COMMENT}  = {
	"word" => [
		"This is the size of word (n-mer) to count. <BR> Thus if you want to count codon frequencies, you should enter 3 here.",
	],
	"infile" => [
		"This is a file previously produced by \'compseq\' that can be used to set the expected frequencies of words in this analysis. <BR> The word size in the current run must be the same as the one in this results file. Obviously, you should use a file produced from protein sequences if you are counting protein sequence word frequencies, and you must use one made from nucleotide frequencies if you and analysing a nucleotide sequence.",
	],
	"frame" => [
		"The normal behaviour of \'compseq\' is to count the frequencies of all words that occur by moving a window of length \'word\' up by one each time. <BR> This option allows you to move the window up by the length of the word each time, skipping over the intervening words. <BR> You can count only those words that occur in a single frame of the word by setting this value to a number other than zero. <BR> If you set it to 1 it will only count the words in frame 1, 2 will only count the words in frame 2 and so on.",
	],
	"ignorebz" => [
		"The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid. <BR> These are not commonly used codes and you may wish not to count words containing them, just noting them in the count of \'Other\' words.",
	],
	"reverse" => [
		"Set this to be true if you also wish to also count words in the reverse complement of a nucleic sequence.",
	],
	"outfile" => [
		"This is the results file.",
	],
	"zerocount" => [
		"You can make the output results file much smaller if you do not display the words with a zero count.",
	],

    };

    $self->{SCALEMIN}  = {

    };

    $self->{SCALEMAX}  = {

    };

    $self->{SCALEINC}  = {

    };

    $self->{INFO}  = {

    };

# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/compseq.pm



    $self->_init_params(@params);

    return $self;
}



1; # Needed to keep compiler happy

