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Contents
module Bio
class Sequence
class NA
# Return the current object or its reverse complement, whichever
# has the sequence that comes first in lexigraphical (alphabetical)
# order
def lowest_lexigraphical_form
rev = self.reverse_complement
to_s < rev.to_s ? self : rev
end
end
class Kmer
# Return a hash of Strings to 0, for each kmer of length k. For instance
# empty_full_kmer_hash(1) => {'A'=>0, 'T'=>0, 'C'=>0, 'G'=>0}
def self.empty_full_kmer_hash(k=4)
return @empty_full_hash.dup unless @empty_full_hash.nil?
counts = {}
ordered_possibilities = %w(A T C G)
keys = ordered_possibilities
(k-1).times do
keys = keys.collect{|k| ordered_possibilities.collect{|n| "#{k}#{n}"}.flatten}.flatten
end
keys.each do |key|
counts[key] = 0
end
counts
end
# Take a kmer hash, and merge those keys to the lowest lexigraphical form
# (See Bio::Sequence::NA#lowest_lexigraphical_form for what this means)
# When 2 keys are reverse complements they get merged into one hash entry,
# where the key is the lowest_lexigraphical_form of the two and the
# value is the sum of the original 2 values
#
# For instance {'A'=>2,'T'=>5} #=> {'A'=>7}
def self.merge_down_to_lowest_lexigraphical_form(hash)
keys = empty_full_kmer_hash.keys
new_hash = {}
hash.each do |kmer, count|
key = Bio::Sequence::NA.new(kmer).lowest_lexigraphical_form.to_s.upcase
new_hash[key] ||= 0
new_hash[key] += count
end
return new_hash
end
end
end
end
Version data entries
5 entries across 5 versions & 1 rubygems