Class: Gff_parser

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(file) ⇒ Gff_parser

Returns a new instance of Gff_parser.



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# File 'lib/gene_assembler/gff_parser.rb', line 4

def initialize(file)
	@dataset=Gff_dataset.new
	File.open(file,'r').each do |line|
		line.chomp!
		if line=~ /^#/ || line=='' #Skip gff comments and blank lines
			next
		end
		if line=~ /^>/ #Skip sequences
			break
		end

		fields=line.split("\t")
		attribs=parse_attribs(fields.last)
		if !attribs.key?('Parent')
			@dataset.add_master_feature(fields[0], fields[1],  fields[2], fields[3], fields[4], fields[5], fields[6], fields[7], attribs)
		else
			@dataset.add_feature(fields[1],  fields[2], fields[3], fields[4], fields[5], fields[6], fields[7], attribs) # Feature is a child so it's put on his parent and it hasn't a parent attrib
		end
	end
	return @dataset
end

Instance Attribute Details

#dataset ⇒ Object

Returns the value of attribute dataset.



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# File 'lib/gene_assembler/gff_parser.rb', line 3

def dataset
  @dataset
end

Instance Method Details

#parse_attribs(attribs) ⇒ Object

Attribs must be a string with info of last column of gff



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# File 'lib/gene_assembler/gff_parser.rb', line 26

def parse_attribs(attribs) #Attribs must be a string with info of last column of gff
	attribs_hash={}
	fields=attribs.split(';')
	fields.each do |attrib|
		attrib_items= attrib.split('=')
		attribs_hash[attrib_items[0]]=attrib_items[1]
	end
	return attribs_hash
end