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

Langue: en

Autres versions - même langue

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

Section: 3 (Bibliothèques de fonctions)

Sommaire

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 (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.