NAME

Bio::Tools::Run::PiseApplication::showfeat

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::showfeat

      Bioperl class for:

        SHOWFEAT        Show features of a sequence. (EMBOSS)


      Parameters: 

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


                showfeat (String)

                init (String)

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

                matchsource (String)
                        Source of feature to display (-matchsource)

                matchtype (String)
                        Type of feature to display (-matchtype)

                matchtag (String)
                        Tag of feature to display (-matchtag)

                matchvalue (String)
                        Value of feature tags to display (-matchvalue)

                sort (Excl)
                        Sort features by Type, Start or Source, Nosort (don't sort - use input order) or join coding regions together and leave other features in the input order -- Sorting features (-sort)

                html (Switch)
                        Use HTML formatting (-html)

                id (Switch)
                        Show sequence ID (-id)

                description (Switch)
                        Show description (-description)

                scale (Switch)
                        Show scale line (-scale)

                width (Integer)
                        Width of graphics lines (-width)

                collapse (Switch)
                        Display features with the same type on one line (-collapse)

                forward (Switch)
                        Display forward sense features (-forward)

                reverse (Switch)
                        Display reverse sense features (-reverse)

                unknown (Switch)
                        Display unknown sense features (-unknown)

                strand (Switch)
                        Display strand of features (-strand)

                source (Switch)
                        Display source of features (-source)

                position (Switch)
                        Display position of features (-position)

                type (Switch)
                        Display type of features (-type)

                tags (Switch)
                        Display tags of features (-tags)

                values (Switch)
                        Display tag values of features (-values)

                outfile (OutFile)
                        Output feature details to a file (-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/wiki/Mailing_lists  - 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 the web:

  http://bugzilla.open-bio.org/

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/showfeat.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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