Bio::Tools::Run::PiseApplication::fmtseq.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

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/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 (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.