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Bio::Tools::Run::PiseApplication::compseq.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::compseqSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::compseqBioperl class for: COMPSEQ Counts the composition of dimer/trimer/etc words in a sequence (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/compseq.html for available values): compseq (String) init (String) sequence (Sequence) sequence [sequences] (-sequence) pipe: seqsfile word (Integer) Word size to consider (e.g. 2=dimer) (-word) infile (InFile) 'compseq' file to use for expected word frequencies (-infile) frame (Integer) Frame of word to look at (0=all frames) (-frame) ignorebz (Switch) Ignore the amino acids B and Z and just count them as 'Other' (-ignorebz) reverse (Switch) Count words in the forward and reverse sense (-reverse) outfile (OutFile) outfile (-outfile) zerocount (Switch) Display the words that have a frequency of zero (-zerocount) 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/compseq.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 $compseq = Bio::Tools::Run::PiseApplication::compseq->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::compseq 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 $compseq = $factory->program('compseq'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::compseq.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre