Bio::Tools::Run::PiseApplication::xblast.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::xblast

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::xblast
       Bioperl class for:
 
         XBLAST  read blast output and mask query
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/xblast.html 
          for available values):
 
 
                 xblast (String)
 
                 blast_output (InFile)
                         Blast Output File (does not work on Blast2 or Blast-Wu output)
                         pipe: blast_output
 
                 query (InFile)
                         Query File
 
                 mask (String)
                         masking character
 
                 fasta (Switch)
                         generate a fasta-format database of the matched segments
 
                 reversed (Switch)
                         generate a reversed output, e.g. masking the non-matched segments.
 
 

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/xblast.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob

new

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