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Bio::Tools::Run::PiseApplication::cons.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::consSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::consBioperl class for: CONS Creates a consensus from multiple alignments (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/cons.html for available values): cons (String) init (String) msf (Sequence) msf -- gapany [set of sequences] (-msf) pipe: seqsfile datafile (Excl) Scoring matrix (-datafile) plurality (Float) Plurality check value (-plurality) identity (Integer) Required number of identities at a position (-identity) outseq (OutFile) outseq (-outseq) pipe: seqfile outseq_sformat (Excl) Output format for: outseq name (String) Name of the consensus sequence (-name) setcase (Float) Define a threshold above which the consensus is given in uppercase (-setcase) auto (String)
FEEDBACK
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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
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/cons.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 $cons = Bio::Tools::Run::PiseApplication::cons->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::cons 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 $cons = $factory->program('cons'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::cons.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre