lib/genevalidator/tabular_parser.rb in genevalidator-1.6.1 vs lib/genevalidator/tabular_parser.rb in genevalidator-1.6.2

@@ -1,44 +1,48 @@
-require 'genevalidator/exceptions'
 require 'csv'
+require 'forwardable'
 
+require 'genevalidator/sequences'
+require 'genevalidator/hsp'
+require 'genevalidator/exceptions'
+
 #
 module GeneValidator
   TabularEntry = Struct.new(:filename, :type, :title, :footer, :xtitle,
                             :ytitle, :aux1, :aux2)
   ##
   # This class parses the tabular output of BLAST (outfmt 6 & 7)
   class TabularParser
+    extend Forwardable
+    def_delegators GeneValidator, :opt, :config
+
     attr_reader :rows
     attr_reader :tab_results
     attr_reader :column_names
     attr_reader :type
 
     ##
     # Initializes the object
-    # +file_content+ : String with the tabular BLAST output
-    # +format+: format of the tabular output (comma/space delimited string)
-    # +type+: :nucleotide or :mrna
-    def initialize(filename, format, type)
+    def initialize(tab_file = opt[:blast_tabular_file],
+                   format = opt[:blast_tabular_options], type = config[:type])
       @column_names = format.gsub(/[-\d]/, '').split(/[ ,]/)
-      @tab_results  = analayse_tabular_file(filename)
-      @rows         = @tab_results.to_enum
       @type         = type
+      @tab_results  = analayse_tabular_file(tab_file)
+      @rows         = @tab_results.to_enum
     end
 
     ##
     #
     def analayse_tabular_file(filename)
-      tab_results  = []
-      file         = File.read(filename)
-      lines        = CSV.parse(file, col_sep: "\t",
-                                     skip_lines: /^#/,
-                                     headers: @column_names)
+      results = []
+      file    = File.read(filename)
+      lines   = CSV.parse(file, col_sep: "\t", skip_lines: /^#/,
+                                headers: @column_names)
       lines.each do |line|
-        tab_results << line.to_hash
+        results << line.to_hash
       end
-      tab_results
+      results
     end
 
     ##
     # move to next query
     def next
@@ -56,21 +60,23 @@
     ##
     #
     def parse_next(query_id = nil)
       current_id = @rows.peek['qseqid']
       return [] if !query_id.nil? && current_id != query_id
-      hits = @tab_results.partition { |h| h['qseqid'] == current_id }[0]
-      hit_seq = initialise_classes(hits)
+      hit_seq = initialise_classes(current_id)
       move_to_next_query
       hit_seq
     rescue StopIteration
       return []
     end
 
+    private
+
     ##
     #
-    def initialise_classes(hits)
+    def initialise_classes(current_id, tab_results = @tab_results)
+      hits = tab_results.partition { |h| h['qseqid'] == current_id }[0]
       hit_list = []
       grouped_hits = hits.group_by { |row| row['sseqid'] }
 
       grouped_hits.each do |query_id, row|
         hit_seq = Sequence.new
@@ -88,10 +94,10 @@
     #
     def initialise_all_hsps(current_query_id, hits, hit_seq)
       hsps = hits.select { |row| row['sseqid'] == current_query_id }
       hsps.each do |row|
         hsp = Hsp.new
-        hsp.init_tabular_attribute(row, type)
+        hsp.init_tabular_attribute(row)
         hit_seq.hsp_list.push(hsp)
       end
     end
   end
 end