NAME

Bio::Tools::Run::PiseApplication::twofeat

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::twofeat

      Bioperl class for:

        TWOFEAT Finds neighbouring pairs of features in sequences (EMBOSS)


      Parameters: 

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


                twofeat (String)

                init (String)

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

                asource (String)
                        Source of first feature (-asource)

                atype (String)
                        Type of first feature (-atype)

                asense (Excl)
                        Sense of first feature -- Sense of first feature (-asense)

                aminscore (Float)
                        Minimum score of first feature (-aminscore)

                amaxscore (Float)
                        Maximum score of first feature (-amaxscore)

                atag (String)
                        Tag of first feature (-atag)

                avalue (String)
                        Value of first feature's tags (-avalue)

                bsource (String)
                        Source of second feature (-bsource)

                btype (String)
                        Type of second feature (-btype)

                bsense (Excl)
                        Sense of second feature -- Sense of second feature (-bsense)

                bminscore (Float)
                        Minimum score of second feature (-bminscore)

                bmaxscore (Float)
                        Maximum score of second feature (-bmaxscore)

                btag (String)
                        Tag of second feature (-btag)

                bvalue (String)
                        Value of second feature's tags (-bvalue)

                overlap (Excl)
                        Specify overlap -- Type of overlap required (-overlap)

                minrange (Integer)
                        The minimum distance between the features (-minrange)

                maxrange (Integer)
                        The maximum distance between the features (-maxrange)

                rangetype (Excl)
                        Specify position -- Positions from which to measure the distance (-rangetype)

                sense (Excl)
                        Specify sense -- Sense of the features (-sense)

                order (Excl)
                        Specify order -- Order of the features (-order)

                twoout (Switch)
                        Do you want the two features written out individually (-twoout)

                typeout (String)
                        Name of the output new feature (-typeout)

                outfile (OutFile)
                        Output feature report (-outfile)

                auto (String)

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 list. Your participation is much appreciated.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

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/

AUTHOR

Catherine Letondal (letondal@pasteur.fr)

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.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

SEE ALSO

• http://bioweb.pasteur.fr/seqanal/interfaces/twofeat.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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