Bio::Tools::Run::PiseApplication::codonw # Bio::Tools::Run::PiseApplication::codonw Bioperl class for: codonw Correspondence Analysis of Codon Usage (J. Peden) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/codonw.html for available values): codonw (String) outfiles (String) seqfile (Sequence) Sequences File gc (Excl) Genetic codes fop_values (Excl) Fop/CBI values cai_values (Excl) CAI values output_type (Switch) Output Computer readable genes (Switch) Concatenate genes (instead of individual genes) CAI (Switch) Codon Adaptation Index (CAI) Fop (Switch) Frequency of OPtimal codons (Fop) CBI (Switch) Codon bias index (CBI) cai_file (InFile) User input file of CAI values (may be computed by a previous COA) pipe: codonw_coa_file fop_file (InFile) User input file of Fop values (may be computed by a previous COA) cbi_file (InFile) User input file of CBI values (may be computed by a previous COA) ENc (Switch) Effective Number of Codons (ENc) GC (Switch) GC content of gene (G+C) GC3s (Switch) GC of silent 3rd codon posit. (GC3s) silent_bc (Switch) Silent base composition all_indices (Switch) All the above indices L_sym (Integer) Number of synonymous codons (L_sym) L_aa (Switch) Total Number of synonymous and non-synonymous codons (L_aa) Hydro (Switch) Hydrophobicity of protein (Hydro) Aromo (Switch) Aromaticity of protein (Aromo) bulk_output_option (Excl) Other output option coa_cu (Switch) COA on codon usage coa_rscu (Switch) COA on RSCU coa_aa (Switch) COA on Amino Acid usage coa_expert (Switch) Generate detailed(expert) statistics on COA coa_axes (Integer) Select number of axis to record coa_num (Integer) Select number of genes to use to identify optimal codons cai_coa (OutFile) pipe: codonw_coa_file

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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/ 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. This software is provided "as is" without warranty of any kind. http://bioweb.pasteur.fr/seqanal/interfaces/codonw.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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