Class: Bio::Ngs::Converter::Qseq

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/ngs/converter.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(default_type = nil) ⇒ Qseq

Returns a new instance of Qseq.



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# File 'lib/bio/ngs/converter.rb', line 24

def initialize(default_type=nil)
  @type=default_type if [:pe, :se].include?(default_type)
  @stats = {}
end

Instance Attribute Details

#buffer ⇒ Object

Source buffer: String with n as line separator File (reading)



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# File 'lib/bio/ngs/converter.rb', line 20

def buffer
  @buffer
end

#stats ⇒ Object (readonly)

keep statistics about total reads, passed filter or not.



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# File 'lib/bio/ngs/converter.rb', line 22

def stats
  @stats
end

#type ⇒ Object

Returns the value of attribute type.



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# File 'lib/bio/ngs/converter.rb', line 21

def type
  @type
end

Instance Method Details

#qseq2fastq_pe(qseq) ⇒ Object

Return the reads in fastq from a paired-end read dataset qseq_line is an Array of strings generated from raw line of qseq file.



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# File 'lib/bio/ngs/converter.rb', line 85

def qseq2fastq_pe(qseq)
  #          qseq = qseq_line.split #logic here
  "@#{qseq[0]}:#{qseq[2]}:#{qseq[3]}:#{qseq[4]}:#{qseq[5]}#0/#{qseq[7]}\n#{qseq[8].gsub(/\./,'N')}\n+\n#{qseq[9]}" if qseq[10]=="1"
end

#qseq2fastq_se(qseq) ⇒ Object

Return the reads in fastq from a single read dataset qseq_line is an Array of strings generated from raw line of qseq file.



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# File 'lib/bio/ngs/converter.rb', line 92

def qseq2fastq_se(qseq)
  #         qseq = qseq_line.split #logic here
  "@#{qseq[0]}:#{qseq[2]}:#{qseq[3]}:#{qseq[4]}:#{qseq[5]}#0/\n#{qseq[8].gsub(/\./,'N')}\n+\n#{qseq[9]}" if qseq[10]=="1"
end

#to_fastq(stats = false) ⇒ Object

Return each line converted in fastq, is a line is not valid because is not good enough that line will return a nil rember to remove the nil values if you are building an array

TODO: benchmark the performances, I suspect this is not ooptimized



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# File 'lib/bio/ngs/converter.rb', line 41

def to_fastq(stats=false)
if (type.nil?)            
  raise "Type of qseq not specifed."
else
  total = 0
  passed = 0
  rejected = 0
  bases_passed_b_quality = 0
  bases_rejected_b_quality = 0
  bases_passed_total = 0
  bases_rejected_total  = 0
  bases_passed_N = 0
  bases_rejected_N = 0
  @buffer.lines do |line|
    qseq_line_array = line.split
    read  = (send "qseq2fastq_#{type}", qseq_line_array)
    total += 1
    if read
      passed+=1
      bases_passed_b_quality += qseq_line_array[9].scan("B").size
      bases_passed_N += qseq_line_array[9].scan("N").size
      bases_passed_total += qseq_line_array[9].size                
    else
      rejected+=1
      bases_rejected_b_quality += qseq_line_array[9].scan("B").size
      bases_rejected_N += qseq_line_array[9].scan("N").size
      bases_rejected_total += qseq_line_array[9].size
    end
    yield read
  end
  @stats={:reads_total=>total,
    :reads_passed=>passed,
    :reads_rejected=>rejected,
    :bases_passed_total => bases_passed_total,
    :bases_rejected_total => bases_rejected_total,
    :bases_passed_with_b_quality => bases_passed_b_quality,
    :bases_rejected_with_b_quality => bases_rejected_b_quality,
    :bases_passed_with_n => bases_passed_N,
    :bases_rejected_with_n => bases_rejected_N}
  end
end