Class: FileParser

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

Direct Known Subclasses

WigfixParser

Constant Summary collapse

@@parsers = 
{}

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(folder, chunk_size) ⇒ FileParser

Returns a new instance of FileParser.



33
34
35
36
37
38
39
 
# File 'lib/anncrsnp/file_parser.rb', line 33

def initialize(folder, chunk_size)
	@folder = folder
	@chunk_size = chunk_size
	@chrom = nil
	@coords = []
	@packs = 0
end

Class Method Details

.available? ⇒ Boolean

PARSER DEPENDANT METHODS

Returns:

  • (Boolean) 


25
26
27
 
# File 'lib/anncrsnp/file_parser.rb', line 25

def self.available?
	return FALSE
end

.format ⇒ Object 



29
30
31
 
# File 'lib/anncrsnp/file_parser.rb', line 29

def self.format
	return 'master'
end

.get_descendants ⇒ Object 



4
5
6
 
# File 'lib/anncrsnp/file_parser.rb', line 4

def self.get_descendants
	return ObjectSpace.each_object(Class).select { |klass| klass < self }
end

.load ⇒ Object 



8
9
10
11
12
13
14
15
16
 
# File 'lib/anncrsnp/file_parser.rb', line 8

def self.load
	path_parsers = File.join(File.dirname(__FILE__), 'file_parsers')
	Dir.glob(path_parsers+'/*').each do |parser|
		require parser
	end
	get_descendants.each do |descendant|
		@@parsers[descendant.format] = descendant if descendant.available?
	end
end

.select(format) ⇒ Object 



18
19
20
 
# File 'lib/anncrsnp/file_parser.rb', line 18

def self.select(format)
	return @@parsers[format]
end

Instance Method Details

#parse(line) ⇒ Object 



41
42
43
 
# File 'lib/anncrsnp/file_parser.rb', line 41

def parse(line)

end

#write_compressed_data ⇒ Object 



45
46
47
48
49
50
51
52
 
# File 'lib/anncrsnp/file_parser.rb', line 45

def write_compressed_data
		p = @packs * @chunk_size
		gz_path = File.join(@folder, "#{@chrom}_#{p}.gz")
    Zlib::GzipWriter.open(gz_path) do |writer|
      Yajl::Encoder.encode(@coords, writer)
    end
    @packs += 1
end