Class: DataIO

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

Overview

Class containing methods for reading and write FASTQ data files.

Instance Method Summary collapse

Constructor Details

#initialize(samples, fastq_files, compress, output_dir) ⇒ DataIO

Internal: Constructor method for DataIO objects.

samples - Array with Sample objects consisting id, index1 and index2 fastq_files - Array of Strings with FASTQ file names of multiplexed data. compress - Symbol indicating if output data should be compressed with

either gzip or bzip2.

output_dir - String with path of output directory.

Returns DataIO object.



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# File 'lib/data_io.rb', line 38

def initialize(samples, fastq_files, compress, output_dir)
  @samples         = samples
  @compress        = compress
  @output_dir      = output_dir
  @suffix1         = extract_suffix(fastq_files, '_R1_')
  @suffix2         = extract_suffix(fastq_files, '_R2_')
  @input_files     = identify_input_files(fastq_files)
  @undetermined    = @samples.size
  @output_file_ios = nil
end

Instance Method Details

#[](key) ⇒ Object

Internal: Getter method that returns a tuple of file handles from key - Sample index Integer key used for lookup.

Returns Array with a tuple of IO objects.



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# File 'lib/data_io.rb', line 107

def [](key)
  @output_file_ios[key]
end

#each ⇒ Object

Internal: Method that reads a Seq entry from each of the file handles in the @input_file_ios Array. Iteration stops when no more Seq entries are found.

Yields an Array with 4 Seq objects.

Returns nothing



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# File 'lib/data_io.rb', line 89

def each
  loop do
    entries = @input_file_ios.each_with_object([]) do |e, a|
      a << e.next_entry
    end

    break if entries.compact.size != 4

    yield entries
  end
end

#open_input_files ⇒ Object

Internal: Method that opens the @input_files for reading.

input_files - Array with input file paths.

Returns an Array with IO objects (file handles).



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# File 'lib/data_io.rb', line 54

def open_input_files
  @input_file_ios = []

  @input_files.each do |input_file|
    @input_file_ios << BioPieces::Fastq.open(input_file)
  end

  yield self
ensure
  close_input_files
end

#open_output_files ⇒ Object

Internal: Method that opens the output files for writing.

Yields a Hash with an incrementing index as keys, and a tuple of file handles as values.



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# File 'lib/data_io.rb', line 70

def open_output_files
  @output_file_ios = {}
  comp             = @compress

  @output_file_ios.merge!(open_output_files_samples(comp))
  @output_file_ios.merge!(open_output_files_undet(comp))

  yield self
ensure
  close_output_files
end