NAME

Bio::Tools::Run::PiseApplication::prettyalign

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::prettyalign

      Bioperl class for:

        SAM     prettyalign - make align2model output more readable (R. Hughey & A. Krogh)

        References:

                R. Hughey and A. Krogh., SAM: Sequence alignment and modeling software system. Technical Report UCSC-CRL-96-22, University of California, Santa Cruz, CA, September 1996. 



      Parameters: 

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


                prettyalign (String)

                a2m (Sequence)
                        Alignment
                        pipe: readseq_ok_alig

                output_format (Excl)
                        Output format (-f and -I)

                column (Switch)
                        Output column indices (-c)

                sequence_index (Switch)
                        Sequence index (number) on each line (-n)

                sequence_ID (Switch)
                        Toggle sequence ID to each line (-i)

                max_inserts (Integer)
                        Max number of insertions printed (-m)

                linelength (Integer)
                        Characters per line (-l)

                space_char (String)
                        Char to show inserts  (-s)

                max_length (Integer)
                        Maximum length of input lines (-L)

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/prettyalign.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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