Module: BioDSL

Defined in:
lib/BioDSL.rb,
lib/BioDSL/csv.rb,
lib/BioDSL/seq.rb,
lib/BioDSL/cary.rb,
lib/BioDSL/fork.rb,
lib/BioDSL/math.rb,
lib/BioDSL/test.rb,
lib/BioDSL/debug.rb,
lib/BioDSL/fasta.rb,
lib/BioDSL/fastq.rb,
lib/BioDSL/config.rb,
lib/BioDSL/mummer.rb,
lib/BioDSL/stream.rb,
lib/BioDSL/command.rb,
lib/BioDSL/filesys.rb,
lib/BioDSL/hamming.rb,
lib/BioDSL/helpers.rb,
lib/BioDSL/tmp_dir.rb,
lib/BioDSL/usearch.rb,
lib/BioDSL/verbose.rb,
lib/BioDSL/version.rb,
lib/BioDSL/commands.rb,
lib/BioDSL/pipeline.rb,
lib/BioDSL/seq/kmer.rb,
lib/BioDSL/seq/trim.rb,
lib/BioDSL/taxonomy.rb,
lib/BioDSL/seq/digest.rb,
lib/BioDSL/serializer.rb,
lib/BioDSL/html_report.rb,
lib/BioDSL/seq/dynamic.rb,
lib/BioDSL/seq/assemble.rb,
lib/BioDSL/commands/dump.rb,
lib/BioDSL/commands/grab.rb,
lib/BioDSL/commands/sort.rb,
lib/BioDSL/seq/ambiguity.rb,
lib/BioDSL/seq/backtrack.rb,
lib/BioDSL/seq/translate.rb,
lib/BioDSL/commands/count.rb,
lib/BioDSL/commands/random.rb,
lib/BioDSL/commands/uclust.rb,
lib/BioDSL/seq/homopolymer.rb,
lib/BioDSL/seq/levenshtein.rb,
lib/BioDSL/commands/add_key.rb,
lib/BioDSL/commands/genecall.rb,
lib/BioDSL/commands/mask_seq.rb,
lib/BioDSL/commands/trim_seq.rb,
lib/BioDSL/commands/degap_seq.rb,
lib/BioDSL/commands/slice_seq.rb,
lib/BioDSL/helpers/aux_helper.rb,
lib/BioDSL/helpers/log_helper.rb,
lib/BioDSL/commands/read_fasta.rb,
lib/BioDSL/commands/read_fastq.rb,
lib/BioDSL/commands/read_table.rb,
lib/BioDSL/commands/uchime_ref.rb,
lib/BioDSL/commands/write_tree.rb,
lib/BioDSL/commands/clip_primer.rb,
lib/BioDSL/commands/filter_rrna.rb,
lib/BioDSL/commands/mean_scores.rb,
lib/BioDSL/commands/merge_table.rb,
lib/BioDSL/commands/plot_scores.rb,
lib/BioDSL/commands/reverse_seq.rb,
lib/BioDSL/commands/slice_align.rb,
lib/BioDSL/commands/trim_primer.rb,
lib/BioDSL/commands/write_fasta.rb,
lib/BioDSL/commands/write_fastq.rb,
lib/BioDSL/commands/write_table.rb,
lib/BioDSL/helpers/email_helper.rb,
lib/BioDSL/commands/classify_seq.rb,
lib/BioDSL/commands/cluster_otus.rb,
lib/BioDSL/commands/collect_otus.rb,
lib/BioDSL/commands/count_values.rb,
lib/BioDSL/commands/merge_values.rb,
lib/BioDSL/commands/plot_heatmap.rb,
lib/BioDSL/commands/plot_matches.rb,
lib/BioDSL/commands/split_values.rb,
lib/BioDSL/helpers/status_helper.rb,
lib/BioDSL/commands/collapse_otus.rb,
lib/BioDSL/commands/unique_values.rb,
lib/BioDSL/commands/usearch_local.rb,
lib/BioDSL/helpers/history_helper.rb,
lib/BioDSL/helpers/options_helper.rb,
lib/BioDSL/commands/assemble_pairs.rb,
lib/BioDSL/commands/complement_seq.rb,
lib/BioDSL/commands/index_taxonomy.rb,
lib/BioDSL/commands/merge_pair_seq.rb,
lib/BioDSL/commands/plot_histogram.rb,
lib/BioDSL/commands/split_pair_seq.rb,
lib/BioDSL/commands/usearch_global.rb,
lib/BioDSL/commands/dereplicate_seq.rb,
lib/BioDSL/commands/align_seq_mothur.rb,
lib/BioDSL/commands/assemble_seq_ray.rb,
lib/BioDSL/commands/assemble_seq_idba.rb,
lib/BioDSL/commands/assemble_seq_spades.rb,
lib/BioDSL/commands/classify_seq_mothur.rb,
lib/BioDSL/commands/plot_residue_distribution.rb,
lib/BioDSL/commands/analyze_residue_distribution.rb

Overview

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #

#

Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #

#

This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. #

#

This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. #

#

You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, # USA. #

#

www.gnu.org/copyleft/gpl.html #

#

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #

#

This software is part of the BioDSL (www.BioDSL.org). #

#

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #

Defined Under Namespace

Modules: Ambiguity, AuxHelper, BackTrack, Commands, Config, Digest, Dynamic, EmailHelper, HistoryHelper, Homopolymer, Kmer, LogHelper, Math, OptionsHelper, StatusHelper, Taxonomy, TmpDir, Translate, Trim Classes: AddKey, AlignSeqMothur, AnalyzeResidueDistribution, Assemble, AssemblePairs, AssembleSeqIdba, AssembleSeqRay, AssembleSeqSpades, BackTrackError, CAry, CAryError, CSV, CSVError, Channel, ClassifySeq, ClassifySeqMothur, ClipPrimer, ClusterOtus, CollapseOtus, CollectOtus, Command, ComplementSeq, Count, CountValues, DegapSeq, DereplicateSeq, Dump, DynamicError, Fasta, FastaError, Fastq, FastqError, Filesys, FilesysError, FilterRrna, Fork, Genecall, Grab, Hamming, HomopolymerError, HtmlReport, IndexTaxonomy, KmerError, Levenshtein, MaskSeq, MeanScores, MergePairSeq, MergeTable, MergeValues, Mummer, Pipeline, PlotHeatmap, PlotHistogram, PlotMatches, PlotResidueDistribution, PlotScores, Random, ReadFasta, ReadFastq, ReadTable, ReverseSeq, Seq, SeqError, Serializer, SliceAlign, SliceSeq, Sort, SplitPairSeq, SplitValues, Stream, TaxonomyError, TrimError, TrimPrimer, TrimSeq, UchimeRef, Uclust, UniqueValues, Usearch, UsearchError, UsearchGlobal, UsearchLocal, WriteFasta, WriteFastq, WriteTable, WriteTree

Constant Summary

ForkError =

Error class for all Fork errors.

Class.new(StandardError)
MummerError =

Error class for Mummer errors.

Class.new(StandardError)
HammingError =

Error class for all exceptions to do with Hamming.

Class.new(StandardError)
VERSION =
'1.0.2'
PipelineError =

Error class for Pipeline errors.

Class.new(StandardError)
DigestError =

Error class for all exceptions to do with Digest.

Class.new(StandardError)
SerializerError =

Error class for Serializer.

Class.new(StandardError)
AssembleError =

Error class for all Assemble errors.

Class.new(StandardError)
AuxiliaryError =
Class.new(StandardError)
OptionError =
Class.new(StandardError)
@@test =

Class variabel visible across the BioDSL module scope.

false
@@debug =

Class variabel visible across the BioDSL module scope.

false
@@verbose =

Class variabel visible across the BioDSL module scope.

false

Class Method Summary collapse

Class Method Details

.debugObject

Class variable getter method.



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# File 'lib/BioDSL/debug.rb', line 34

def self.debug
  @@debug
end

.debug=(x) ⇒ Object

Class variable setter method.



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# File 'lib/BioDSL/debug.rb', line 39

def self.debug=(x)
  @@debug = x
end

.testObject

Class variable getter method.



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# File 'lib/BioDSL/test.rb', line 34

def self.test
  @@test
end

.test=(x) ⇒ Object

Class variable setter method.



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# File 'lib/BioDSL/test.rb', line 39

def self.test=(x)
  @@test = x
end

.verboseObject

Class variable getter method.



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# File 'lib/BioDSL/verbose.rb', line 34

def self.verbose
  @@verbose
end

.verbose=(x) ⇒ Object

Class variable setter method.



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# File 'lib/BioDSL/verbose.rb', line 39

def self.verbose=(x)
  @@verbose = x
end