NAME

Bio::Tools::Run::PiseApplication::fmtseq

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::fmtseq

      Bioperl class for:

        fmtseq  sequence conversion (J. R. Knight)


      Parameters: 

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


                fmtseq (String)

                seq (InFile)
                        Sequence File
                        pipe: readseq_ok_alig

                outfile (OutFile)
                        pipe: seqsfile

                outformat (Excl)
                        Output Sequence Format

                gapin (Excl)
                        Set the gap symbol for the input (-gapin)

                informat (Excl)
                        Input sequence format (-inf[ormat])

                caselower (Switch)
                        convert to lowercase (-c)

                CASEUPPER (Switch)
                        convert to upper case (-C)

                degap (Switch)
                        Remove gaps from sequences (-degap)

                gapout (Excl)
                        Set the gap symbol for the output (-gapout)

                list (Switch)
                        Only list sequence information (-li)

                long (Switch)
                        Long form conversion (input header included as comment) (-long)

                raw (Excl)
                        Gaps in sequences (-raw)

                reverse (Switch)
                        Reverse-complement each sequence (-re)

                interleave (Excl)
                        Output interleaved sequences (-interleave)

                width (Integer)
                        Sequence line width (-width)

                tab (Integer)
                        Indent sequence (-tab)

                colspace (Integer)
                        Add space columms in sequence lines (-colspace)

                gapcount (Excl)
                        Count gap chars in sequence numbers (-gapcount)

                nameleft (Integer)
                        Name on left side (-nameleft)

                nameright (Integer)
                        Name on left side (-nameright)

                nametop (Switch)
                        Name at top (-nametop)

                numleft (Excl)
                        Sequence index on left/right side

                numtop (Excl)
                        Index on top/bottom

                match (Switch)
                        Replace matches to first sequence with . (-match)

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

                skipempty (Switch)
                        Do not output lines with only gap characters (-skipempty)

                bigalign (Switch)
                        Convert FASTA program output to big alignment (-bigalign)

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/fmtseq.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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