Top Level Namespace

Defined Under Namespace

Modules: Ms Classes: Hash

Instance Method Summary collapse

Instance Method Details

#basename(file) ⇒ Object 



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# File 'bin/peptide_hit_qvalues_to_spectral_counts_table.rb', line 28

def basename(file)
  base = file.chomp(File.extname(file))
  base=base.chomp(File.extname(base)) if File.extname(base) == '.phq'
  base
end

#putsv(*args) ⇒ Object 



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# File 'bin/peptide_hit_qvalues_to_spectral_counts_table.rb', line 22

def putsv(*args)
  if $VERBOSE
    puts(*args) ; $stdout.flush
  end
end

#write_subset(sample_to_pephits, outfile = "peptidecentric_subset.yml") ⇒ Object 



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# File 'bin/peptide_hit_qvalues_to_spectral_counts_table.rb', line 61

def write_subset(sample_to_pephits, outfile="peptidecentric_subset.yml")
  aaseqs_to_prots = {} 
  sample_to_pephits.map(&:last).flatten(1).each do |pephit|
    aaseqs_to_prots[pephit.aaseq] = pephit.proteins.map(&:id)
  end
  File.open(outfile,'w') do |out| 
    aaseqs_to_prots.each do |k,v| 
      out.puts(%Q{#{k}: #{v.join("\t") }}) 
    end
  end
end