NAME

Bio::Tools::Run::PiseApplication::readseq

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::readseq

      Bioperl class for:

        READSEQ  (D. Gilbert)


      Parameters: 

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


                readseq (String)

                seq (InFile)
                        Sequence File
                        pipe: readseq_ok_alig

                outfile (OutFile)
                        pipe: seqfile

                outformat (Excl)
                        Output Sequence Format

                items (String)
                        select Item number(s) from several

                allseq (Switch)

                lowcase (Switch)
                        Change to lower case (-c)

                uppcase (Switch)
                        Change to UPPER case (-C)

                degap (Switch)
                        Remove gap symbols (-degap)

                reverse (Switch)
                        Change to Reverse-complement (-r)

                listonly (Switch)
                        List sequences only (-l)

                width (Integer)
                        Sequence line width (-width)

                tab (Integer)
                        Left indent (-tab)

                col (Integer)
                        Column space within sequence line on output (-col)

                gap (Integer)
                        Count gap chars in sequence numbers (-gap)

                nameleft (Excl)
                        Name on left/right side

                nametop (Switch)
                        Name at top (-nametop)

                numleft (Excl)
                        Sequence index on left/right side

                numtop (Excl)
                        Index on top/bottom

                match (Switch)
                        Use match base (.) for 2..n species (-match)

                interline (Integer)
                        How many blank line(s) between sequence blocks

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/readseq.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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