ExonContainer.rb in bio-polyploid-tools-0.8.0

- old
+ new

@@ -17,19 +17,35 @@
       @primer_3_min_seq_length = 50
     end
 
     def gene_models(path)
       @gene_models_db = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
+      @gene_models_db.index
       @gene_models_path = path
     end
 
     #Returns the sequence for a region in the gene models (exon)
     def gene_model_sequence(region)
-      #puts region
-      seq=@gene_models_db.fetch_sequence(region)
+      #puts "Region: "
+      #puts region.inspect
+      target_reg = @gene_models_db.index.region_for_entry(region.entry)
+      #puts target_reg.inspect
+      region.end = target_reg.length if region.end > target_reg.length
+      #entries[region.entry]
 
-
+      seq=@gene_models_db.fetch_sequence(region)
+      #puts "sequence: "
+      #This is a patch that we need to fix in biosamtools: 
+      #puts seq
+      index = seq.index('>')
+      if(index )
+        index -= 1
+        #puts "Index: #{index}"
+        seq = seq.slice(0..index) 
+      end
+      #puts seq
+      seq
     end
 
     #Sets the reference file for the gene models
     def chromosomes(path)
       @chromosomes_db = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
@@ -38,14 +54,14 @@
 
     #Retunrs the sequence for a region in the gene models (exon)
     def chromosome_sequence(region)
       left_pad = 0
       #TODO: Padd if it goes to the right
-      if(region.start < 0)
+      if(region.start < 1)
         left_pad = region.start * -1
         left_pad += 1
-        region.start = 0
+        region.start = 1
       end
       str = "-" * left_pad << @chromosomes_db.fetch_sequence(region)
       #str << "n" * (region.size - str.size + 1) if region.size > str.size
       str
     end 
@@ -114,16 +130,21 @@
     def print_fasta_snp_exones (file)
       @missing_exons = Set.new unless @missing_exons
       @snp_map.each do | gene, snp_array|
         snp_array.each do |snp|
           #file.puts snp.primer_fasta_string 
-       
+          #puts "In print_fast_np_exones"
+          #puts snp.inspect
+
           begin 
             file.puts snp.aligned_sequences_fasta
           rescue Exception=>e
             @missing_exons << snp.to_s
-            $stderr.puts e.to_s
+            $stderr.puts "print_fasta_snp_exones:" + snp.to_s + ":" + e.to_s
+            $stderr.puts "Local position: #{snp.local_position}"
+            $stderr.puts "Local position: #{snp.parental_sequences.to_s}"
+            $stderr.puts e.backtrace
           end
         end
       end
     end
 
@@ -141,11 +162,13 @@
               file.puts string
               added += 1
             end 
            rescue Exception=>e
               @missing_exons << snp.to_s
+             # $stderr.puts ""
 
-              $stderr.puts e.to_s
+              $stderr.puts "print_primer_3_exons: #{e.to_s} : snp.to_s"
+              $stderr.puts e.backtrace
             end
         end 
       end
       return added
     end
\ No newline at end of file