Class: Bio::KmerMultipleAbundanceHash

Inherits:
Hash
  • Object
show all
Includes:
FinishM::Logging
Defined in:
lib/kmer_multi_abundance_file.rb

Overview

A class to work with a kmer abundance file format, where the kmer is first, then each abundance after that (no headings, space separated)

Class Method Summary collapse

Instance Method Summary collapse

Methods included from FinishM::Logging

#log

Class Method Details

.parse_from_file(path) ⇒ Object 



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# File 'lib/kmer_multi_abundance_file.rb', line 9

def self.parse_from_file(path)
  obj = self.new
  kmer_length = nil
  num_abundances = nil
  CSV.foreach(path, :col_sep => ' ') do |row|
    kmer = row[0].upcase
    abundances = row[1...row.length]

    kmer_length ||= kmer.length
    if kmer.length != kmer_length
      raise "inconsistent length of kmer found in kmer abundance file, in line: #{row.inspect}"
    end
    num_abundances ||= abundances.length
    if num_abundances != abundances.length
      raise "inconsistent number of abundances found in kmer abundance file, in line: #{row.inspect}"
    end
    obj[kmer] = abundances
  end
  return obj
end

Instance Method Details

#[](kmer) ⇒ Object 



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# File 'lib/kmer_multi_abundance_file.rb', line 42

def [](kmer)
  abundances = super(kmer.upcase)
  abundances ||= [0]*number_of_abundances
  return abundances
end

#kmer_length ⇒ Object 



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# File 'lib/kmer_multi_abundance_file.rb', line 30

def kmer_length
  each do |kmer, abundances|
    return kmer.length
  end
end

#number_of_abundances ⇒ Object 



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# File 'lib/kmer_multi_abundance_file.rb', line 36

def number_of_abundances
  each do |kmer, abundances|
    return abundances.length
  end
end