gffparser.rb in bio-gff3-0.9.0

- old
+ new

@@ -29,16 +29,17 @@
           return if rec.comment # skip GFF comments
           id = Helpers::Record::formatID(rec)
           @count_ids.add(id)
           @count_seqnames.add(rec.seqname)
 
-          is_component = COMPONENT_TYPES.include?(rec.feature_type)
+          is_component = COMPONENT_TYPES.include?(rec.feature_type.upcase)
           if is_component
             # check for container ID
             warn("Container <#{rec.feature_type}> has no ID, so using sequence name instead",id) if rec.id == nil
             @componentlist[id] = rec
-            info "Added #{rec.feature_type} with component ID #{id}"
+            info "Added feature <#{rec.feature_type}> with component ID",id
+            # $stderr.print rec
           end 
           case rec.feature_type
             when 'gene' || 'SO:0000704'
               @orflist.add(id,rec)
             when 'mRNA' || 'SO:0000234'
@@ -54,11 +55,11 @@
           end
         end
 
         def show_unrecognized_features 
           @unrecognized_features.keys.each do | k |
-            warn "Feature has no match",k if k
+            warn "Unknown feature is ignored",k if k
           end
         end
 
         def read_fasta
           if @options[:fasta_filename]
@@ -129,9 +130,10 @@
 
         # Yield a unique description and the sequence
         def each_CDS_seq
           each_CDS do | id, reclist, component |
             if component
+              # p id,reclist,component
               sequence = @sequencelist[component.seqname]
               # p sequence
               if sequence
                 seq = assemble(sequence,component.start,reclist,@options.merge(:codonize=>true))
                 if seq.size % 3 != 0