Module: Bioinform

Defined in:

lib/bioinform/background.rb,
lib/bioinform.rb,
lib/bioinform/cli.rb,
lib/bioinform/errors.rb,
lib/bioinform/support.rb,
lib/bioinform/version.rb,
lib/bioinform/alphabet.rb,
lib/bioinform/validator.rb,
lib/bioinform/cli/pcm2pwm.rb,
lib/bioinform/data_models/pm.rb,
lib/bioinform/data_models/pcm.rb,
lib/bioinform/data_models/ppm.rb,
lib/bioinform/data_models/pwm.rb,
lib/bioinform/cli/split_motifs.rb,
lib/bioinform/cli/convert_motif.rb,
lib/bioinform/parsers/matrix_parser.rb,
lib/bioinform/parsers/motif_splitter.rb,
lib/bioinform/data_models/named_model.rb,
lib/bioinform/formatters/motif_formatter.rb,
lib/bioinform/formatters/transfac_formatter.rb,
lib/bioinform/formatters/consensus_formatter.rb,
lib/bioinform/formatters/pretty_matrix_formatter.rb,
lib/bioinform/conversion_algorithms/pcm2ppm_converter.rb,
lib/bioinform/conversion_algorithms/pcm2pwm_converter.rb,
lib/bioinform/conversion_algorithms/ppm2pcm_converter.rb,
lib/bioinform/conversion_algorithms/pwm2pcm_converter.rb,
lib/bioinform/conversion_algorithms/pcm2pwm_mara_converter.rb,
lib/bioinform/conversion_algorithms/pwm2iupac_pwm_converter.rb

Overview

TODO: generalize for the case of different alphabet

Defined Under Namespace

Modules: Background, CLI, ConversionAlgorithms, FrequencyCalculations, IUPAC, MotifModel, Support Classes: ComplementableAlphabet, ConsensusFormatter, Error, Frequencies, MatrixParser, MotifFormatter, MotifSplitter, PrettyMatrixFormatter, TransfacFormatter, ValidationError, ValidationResult, Validator, WordwiseBackground

Constant Summary

VERSION =

"0.3.1"

NucleotideAlphabet =

ComplementableAlphabet.new([:A,:C,:G,:T], [:T,:G,:C,:A])

NucleotideAlphabetWithN =

ComplementableAlphabet.new([:A,:C,:G,:T,:N], [:T,:G,:C,:A,:N])

IUPACAlphabet =

ComplementableAlphabet.new( iupac_letters,
iupac_letters.map{|letter| IUPAC.complement_iupac_letter(letter) } )