Module: FastqAssessment

Defined in:
lib/fastq_assessment.rb

Defined Under Namespace

Classes: FastqStats, ReadPositionStats

Instance Method Summary collapse

Instance Method Details

#generate_quality_stats_for_read(fastq_file, quality_scale, quality_cutoff = 30) ⇒ Object 



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# File 'lib/fastq_assessment.rb', line 6

def generate_quality_stats_for_read(fastq_file, quality_scale, quality_cutoff = 30)
  fastq_stats = FastqStats.new()
  fastq_stats.read_position_stats = Array.new
  if quality_scale == 64
    qual_stats = `fastx_quality_stats -i #{fastq_file}`
  else
    qual_stats = `fastx_quality_stats -Q 33 -i #{fastq_file}`
  end
  read_positions = qual_stats.split("\n")
  qualities_at_read_positions = Array.new
  read_positions.each do |read_position|
    qual_stats = read_position.split(/\s+/)
    mean_quality = qual_stats[5].to_f
    median_quality = qual_stats[7].to_f
    first_quartile = qual_stats[6].to_f
    third_quartile = qual_stats[8].to_f
    qualities_at_read_positions << mean_quality
    fastq_stats.read_position_stats << ReadPositionStats.new(
      mean_quality,
      median_quality,
      first_quartile,
      third_quartile
      )
  end
  # determine mean quality
  fastq_stats.mean_quality = qualities_at_read_positions.mean
  # determine  position where quality in a 5 position window drops below 20
  position = 0
  qualities_at_read_positions.each_cons(5) do |window|
    position += 1
    if window.mean < quality_cutoff && position > 15
      fastq_stats.position_where_quality_lt_20 = position
      break
    end
  end
  return fastq_stats
end

#percentage_compared_to_raw(processed_fastq_file, raw_fastq_file) ⇒ Object 



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# File 'lib/fastq_assessment.rb', line 44

def percentage_compared_to_raw(processed_fastq_file, raw_fastq_file)
  file_lines_processed = `wc -l #{processed_fastq_file}`.split(" ").first.to_f
  file_lines_raw = `wc -l #{raw_fastq_file}`.split(" ").first.to_f
  percentage_reduction = (file_lines_processed/file_lines_raw*100).to_i
end