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Bio::Tools::Run::PiseApplication::sreformat.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::sreformatSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::sreformatBioperl class for: HMMER sreformat - convert sequence file to different format (S. Eddy) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/sreformat.html for available values): sreformat (String) seqfile (InFile) Sequence(s) file pipe: hmmer_alig output_format (Excl) output format dna (Switch) DNA (-d) lowercase (Switch) Convert all sequence residues to lower case (-l) rna (Switch) RNA (-r) uppercase (Switch) Convert all sequence residues to upper case (-u) iupac_convert (Switch) Convert DNA non-IUPAC characters (such as X's) to N's (-x) pfam (Switch) (--pfam) sam (Switch) (--sam) samfrac (Float) (--samfrac x)
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.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/sreformat.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 $sreformat = Bio::Tools::Run::PiseApplication::sreformat->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::sreformat 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 $sreformat = $factory->program('sreformat'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::sreformat.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre