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Bio::Tools::Run::PiseApplication::msbar.3pm
Langue: en
Version: 2005-10-09 (mandriva - 01/05/08)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::Tools::Run::PiseApplication::msbarSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::msbarBioperl class for: MSBAR Mutate sequence beyond all recognition (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/msbar.html for available values): msbar (String) init (String) sequence (Sequence) sequence -- any [sequences] (-sequence) pipe: seqsfile count (Integer) Number of times to perform the mutation operations (-count) point (List) Types of point mutations to perform -- Point mutation operations [select values] (-point) block (List) Types of block mutations to perform -- Block mutation operations [select values] (-block) inframe (Switch) Do 'codon' and 'block' operations in frame (-inframe) codon (List) Types of codon mutations to perform -- Codon mutation operations [select values] (-codon) minimum (Integer) Minimum size for a block mutation (-minimum) maximum (Integer) Maximum size for a block mutation (-maximum) other (Sequence) Other sequences that the mutated result should not match (-other) outseq (OutFile) outseq (-outseq) pipe: seqsfile outseq_sformat (Excl) Output format for: outseq auto (String)
FEEDBACK
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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.bioperl.org/
AUTHOR
Catherine Letondal (letondal@pasteur.fr)COPYRIGHT
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
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- http://bioweb.pasteur.fr/seqanal/interfaces/msbar.html
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- Bio::Tools::Run::PiseApplication
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- Bio::Tools::Run::AnalysisFactory::Pise
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- Bio::Tools::Run::PiseJob
new
Title : new() Usage : my $msbar = Bio::Tools::Run::PiseApplication::msbar->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::msbar 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 $msbar = $factory->program('msbar'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::msbar.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre