Bio::Tools::Run::PiseApplication::pratt.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::pratt

SYNOPSIS

   #

DESCRIPTION

Bio::Tools::Run::PiseApplication::pratt 
       Bioperl class for:
 
         Pratt   pattern discovery (K. Sturzrehm, I. Jonassen)
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/pratt.html 
          for available values):
 
 
                 pratt (String)
 
                 seq (Sequence)
                         Sequence File
 
                 seqformat (Excl)
                         Sequence File format
 
                 CM (Integer)
                         CM: min Nr of Seqs to Match (between 2 and 4)
 
                 Cpct (Integer)
                         C%: min Percentage Seqs to Match
 
                 PP (Excl)
                         PP: pos in seq
 
                 PF (InFile)
                         PF: Restriction File name (if PP not off)
 
                 PL (Integer)
                         PL: max Pattern Length
 
                 PN (Integer)
                         PN: max Nr of Pattern Symbols
 
                 PX (Integer)
                         PX: max Nr of consecutive x's
 
                 FN (Integer)
                         FN: max Nr of flexible spacers
 
                 FL (Integer)
                         FL: max Flexibility
 
                 FP (Integer)
                         FP: max Flex.Product
 
                 BI (Switch)
                         BI: Input Pattern Symbol File?
 
                 BF (InFile)
                         BF: Input Pattern Symbol File name (if BI on)
 
                 BN (Integer)
                         BN: Nr of Pattern Symbols Initial Search
 
                 S (Excl)
                         S: Scoring
 
                 treefile (InFile)
                         Tree File (if Scoring = tree)
 
                 distfile (InFile)
                         Distances File (if Scoring = dist)
 
                 swissprotdb (String)
 
                 Z0 (Integer)
                         Z0
 
                 Z1 (Integer)
                         Z1
 
                 Z2 (Integer)
                         Z2
 
                 Z3 (Integer)
                         Z3
 
                 G (Excl)
                         G: Pattern Graph from:
 
                 GF (InFile)
                         Alignment or Query Filename (if G set to al or query)
 
                 E (Integer)
                         E: Search Greediness
 
                 R (Switch)
                         R: Pattern Refinement
 
                 RG (Switch)
                         RG: Generalise ambiguous symbols (if Pattern Refinement on)
 
                 OF (OutFile)
                         OF: Output Filename
 
                 OP (Switch)
                         OP: PROSITE Pattern Format
 
                 ON (Integer)
                         ON: max number patterns
 
                 OA (Integer)
                         OA: max number Alignments
 
                 M (Switch)
                         M: Print Patterns in sequences
 
                 MR (Integer)
                         MR: ratio for printing
 
                 MV (Switch)
                         MV: print vertically

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

new

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