Bio::Tools::Run::PiseApplication::infoalign.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::infoalign

SYNOPSIS

   #

DESCRIPTION

Bio::Tools::Run::PiseApplication::infoalign 
       Bioperl class for:
 
         INFOALIGN       Information on a multiple sequence alignment (EMBOSS)
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/infoalign.html 
          for available values):
 
 
                 infoalign (String)
 
                 init (String)
 
                 sequence (Sequence)
                         sequence -- gapany [set of sequences] (-sequence)
                         pipe: seqsfile
 
                 refseq (String)
                         The number or the name of the reference sequence (-refseq)
 
                 matrix (Excl)
                         Similarity scoring Matrix file (-matrix)
 
                 plurality (Float)
                         Plurality check % for consensus (-plurality)
 
                 identity (Float)
                         Required % of identities at a position fro consensus (-identity)
 
                 outfile (OutFile)
                         Output sequence details to a file (-outfile)
 
                 html (Switch)
                         Format output as an HTML table (-html)
 
                 only (Switch)
                         Display the specified columns (-only)
 
                 heading (Switch)
                         Display column headings (-heading)
 
                 usa (Switch)
                         Display the USA of the sequence (-usa)
 
                 name (Switch)
                         Display 'name' column (-name)
 
                 seqlength (Switch)
                         Display 'seqlength' column (-seqlength)
 
                 alignlength (Switch)
                         Display 'alignlength' column (-alignlength)
 
                 gaps (Switch)
                         Display number of gaps (-gaps)
 
                 gapcount (Switch)
                         Display number of gap positions (-gapcount)
 
                 idcount (Switch)
                         Display number of identical positions (-idcount)
 
                 simcount (Switch)
                         Display number of similar positions (-simcount)
 
                 diffcount (Switch)
                         Display number of different positions (-diffcount)
 
                 change (Switch)
                         Display % number of changed positions (-change)
 
                 description (Switch)
                         Display 'description' column (-description)
 
                 auto (String)

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

new

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