Module: Bio::Jaspar

Defined in:
lib/bio-jaspar/jaspar.rb

Overview

JASPAR 2014 module

Provides read access to a JASPAR5 formatted database.

This module is a direct import of Bio.motifs.jaspar module in Biopython. The following document contains excerpts from Bio.motifs.jaspar module in Biopython.

Defined Under Namespace

Classes: Motif, Record

Constant Summary collapse

DNA =

Unambiguous DNA bases

Bio::Motifs::Alphabet.new.IUPAC_unambiguous_dna
JASPAR_ORDERED_DNA_LETTERS =

JASPAR OUTPUT specific DNA bases

["A","C","G","T"]

Class Method Summary collapse

Class Method Details

.calculate_pseudocounts(motif) ⇒ Object

Return pseudocounts of a given JASPAR motif



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# File 'lib/bio-jaspar/jaspar.rb', line 240

def Jaspar.calculate_pseudocounts(motif)
	alphabet = motif.alphabet
	background = motif.background

	total = 0
	(0...motif.length).each do |i|
		total += alphabet.letters.map { |letter| motif.counts[letter][i].to_f }.inject(:+)
	end

	avg_nb_instances = total / motif.length
	sq_nb_instances = Math.sqrt(avg_nb_instances)

	if background
		background = Hash[background]
	else
		background = Hash[alphabet.letters.sort.map { |l| [l, 1.0] }]
	end

	total = background.values.inject(:+)
	pseudocounts = {}

	alphabet.letters.each do |letter|
		background[letter] /= total
		pseudocounts[letter] = sq_nb_instances * background[letter]
	end

	return pseudocounts
end

.read(handle, format) ⇒ Object

Return the record of PFM(s). Call the appropriate routine based on the format passed



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# File 'lib/bio-jaspar/jaspar.rb', line 190

def Jaspar.read(handle, format)
	format = format.downcase
	if format == "pfm"
		record = _read_pfm(handle)
		return record
	elsif format == "sites"
		record = _read_sites(handle)
		return record
	elsif format == "jaspar"
		record = _read_jaspar(handle)
		return record
	else
		raise ArgumentError, "Unknown JASPAR format #{format}"
	end
			
end

.split_jaspar_id(id) ⇒ Object

Components are base ID and version number, e.g. ‘MA0047.2’ is returned as (‘MA0047’, 2).



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# File 'lib/bio-jaspar/jaspar.rb', line 273

def Jaspar.split_jaspar_id(id)
	id_split = id.split(".")

	base_id = nil
	version = nil

	if id_split.length == 2
		base_id = id_split[0]
		version = id_split[1]
	else
		base_id = id
	end

	return base_id, version
end

.write(motifs, format) ⇒ Object

Return the representation of motifs in “pfm” or “jaspar” format.



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# File 'lib/bio-jaspar/jaspar.rb', line 208

def Jaspar.write(motifs, format)
	letters = JASPAR_ORDERED_DNA_LETTERS
	lines = []
	if format == "pfm"
		motif = motifs[0]
		counts = motif.counts
		letters.each do |letter|
			terms = counts[letter].map { |value| "%6.2f" % value }
			line = "#{terms.join(" ")}\n"
			lines << line
		end
	elsif format == "jaspar"
		motifs.each do |m|
			counts = m.counts
			line = ">#{m.matrix_id} #{m.name}\n"
			lines << line

			letters.each do |letter|
				terms = counts[letter].map { |value| "%6.2f" % value }
				line = "#{letter} [#{terms.join(" ")}]\n"
				lines << line
			end
		end
	else
		raise ArgumentError, "Unknown JASPAR format #{format}"
	end
		
	text = lines.join("")
	return text	
end