Class: WigfixParser

Inherits:
FileParser show all
Defined in:
lib/anncrsnp/file_parsers/wigfix_parser.rb

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from FileParser

get_descendants, load, select, #write_compressed_data

Constructor Details

#initialize(folder, chunk_size) ⇒ WigfixParser

Returns a new instance of WigfixParser.



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# File 'lib/anncrsnp/file_parsers/wigfix_parser.rb', line 2

def initialize(folder, chunk_size)
	super
	@start = 1
	@step = 1
end

Class Method Details

.available? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/anncrsnp/file_parsers/wigfix_parser.rb', line 8

def self.available?
	return TRUE
end

.format ⇒ Object 



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# File 'lib/anncrsnp/file_parsers/wigfix_parser.rb', line 12

def self.format
	return 'wigfix'
end

Instance Method Details

#get_data ⇒ Object 



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# File 'lib/anncrsnp/file_parsers/wigfix_parser.rb', line 62

def get_data
	return @coords
end

#parse(line) ⇒ Object 



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# File 'lib/anncrsnp/file_parsers/wigfix_parser.rb', line 16

def parse(line)
	#fixedStep chrom=chr11 start=60001 step=1
	if line.include?('fixedStep')
		line =~ /fixedStep chrom=(\S+) start=(\d+) step=(\d+)/
		if !@chrom.nil? && @chrom != $1 #We change of chromosome, we write the buffered coordinates
			#puts "=> #{@packs}\t#{@start}\tx"
			#puts @coords.first.inspect
			#puts @coords.last.inspect
			write_compressed_data
			@coords = []
		end
		@chrom = $1
		last_start = @start
		@start = $2.to_i
		diff = @start - last_start #Create dummy files to fill gaps on coordinate scores
		if diff >= @chunk_size
			(diff/@chunk_size).times do 
				#puts "=> #{@packs}\t#{@start}\td"
				#puts @coords.first.inspect
				#puts @coords.last.inspect
				write_compressed_data
				@coords = []
			end
		else
			if @start/@chunk_size != last_start/@chunk_size #Current coordinate belongs to another pack that the previous, write the buffered coordinates
				#puts "=> #{@packs}\t#{@start}\te"
				#puts @coords.first.inspect
				#puts @coords.last.inspect
				write_compressed_data
				@coords = []
			end
		end
		@step = $3.to_i
	else
		if @start % @chunk_size == 0 # We have reached the chun size, write it to disk
			#puts "=> #{@packs}\t#{@start}\tl"
			#puts @coords.first.inspect
			#puts @coords.last.inspect
			write_compressed_data
			@coords = []
		end
		@coords << [@start, line.to_f]
		@start += @step
	end
end