Bio::Tools::Run::PiseApplication::sreformat.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::sreformat

SYNOPSIS

   #

DESCRIPTION

Bio::Tools::Run::PiseApplication::sreformat 
       Bioperl class for:
 
         HMMER   sreformat - convert sequence file to different format (S. Eddy)
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/sreformat.html 
          for available values):
 
 
                 sreformat (String)
 
                 seqfile (InFile)
                         Sequence(s) file
                         pipe: hmmer_alig
 
                 output_format (Excl)
                         output format
 
                 dna (Switch)
                         DNA (-d)
 
                 lowercase (Switch)
                         Convert all sequence residues to lower case (-l)
 
                 rna (Switch)
                         RNA (-r)
 
                 uppercase (Switch)
                         Convert all sequence residues to upper case (-u)
 
                 iupac_convert (Switch)
                         Convert DNA non-IUPAC characters (such as X's) to N's (-x)
 
                 pfam (Switch)
                         (--pfam)
 
                 sam (Switch)
                         (--sam)
 
                 samfrac (Float)
                         (--samfrac x)

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/sreformat.html
•
Bio::Tools::Run::PiseApplication
•
Bio::Tools::Run::AnalysisFactory::Pise
•
Bio::Tools::Run::PiseJob

new

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