Class: Fastq

Inherits:
Object
  • Object
show all
Defined in:
lib/nugen_barcode_splitter/fastq.rb

Instance Method Summary collapse

Constructor Details

#initialize(filename) ⇒ Fastq

Returns a new instance of Fastq.

Raises:

  • (RuntimeError) 


2
3
4
5
6
7
 
# File 'lib/nugen_barcode_splitter/fastq.rb', line 2

def initialize(filename)
  @filehandle = File.open(filename, "r")
  line = @filehandle.readline()
  raise RuntimeError, "Invalid fastq file!" if !line.include?("@")
  @filehandle.pos = 0
end

Instance Method Details

#add(num, outdir) ⇒ Object 



9
10
11
12
13
14
15
16
17
18
19
20
21
 
# File 'lib/nugen_barcode_splitter/fastq.rb', line 9

def add(num, outdir)
  bases = "N" * num
  qualities = "@" * num
  outfile = File.open(outdir, 'w')

  while !@filehandle.eof?
    outfile.write(@filehandle.readline)
    outfile.write("#{bases}" + @filehandle.readline)
    outfile.write(@filehandle.readline)
    outfile.write("#{qualities}" + @filehandle.readline)
  end
  outfile.close()
end

#close ⇒ Object 



23
24
25
 
# File 'lib/nugen_barcode_splitter/fastq.rb', line 23

def close()
  @filehandle.close()
end