Class: Bio::FastQC::Data

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/fastqc/data.rb

Class Method Summary collapse

Class Method Details

.filenotfound(file) ⇒ Object 



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# File 'lib/bio/fastqc/data.rb', line 35

def filenotfound(file)
  raise "FastQC data file fastqc_data.txt not found, input file: #{file}"
end

.read(file) ⇒ Object 



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# File 'lib/bio/fastqc/data.rb', line 9

def read(file)
  read_zipfile(file)
rescue Zip::Error
  read_flatfile(file)
rescue Errno::EISDIR
  read_dir(file)
end

.read_dir(file) ⇒ Object 



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# File 'lib/bio/fastqc/data.rb', line 29

def read_dir(file)
  open(File.join(file, "fastqc_data.txt")).read
rescue Errno::ENOENT
  filenotfound(file)
end

.read_flatfile(file) ⇒ Object 



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# File 'lib/bio/fastqc/data.rb', line 25

def read_flatfile(file)
  open(file).read
end

.read_zipfile(file) ⇒ Object 



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# File 'lib/bio/fastqc/data.rb', line 17

def read_zipfile(file)
  Zip::File.open(file) do |zipfile|
    d = zipfile.glob('*/fastqc_data.txt').first
    filenotfound(file) if !d
    d.get_input_stream.read
  end
end