ExonContainer.rb in bio-polyploid-tools-0.2.3

- old
+ new

@@ -15,24 +15,24 @@
       @snp_map = Hash.new 
       @snp_contigs
     end
 
     def gene_models(path)
-      @gene_models_db = Bio::DB::Fasta::FastaFile.new(path)
+      @gene_models_db = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
       @gene_models_path = path
     end
 
-    #Retunrs the sequence for a region in the gene models (exon)
+    #Returns the sequence for a region in the gene models (exon)
     def gene_model_sequence(region)
       seq=@gene_models_db.fetch_sequence(region)
 
 
     end
 
     #Sets the reference file for the gene models
     def chromosomes(path)
-      @chromosomes_db = Bio::DB::Fasta::FastaFile.new(path)
+      @chromosomes_db = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
       @chromosomes_path = path
     end
 
     #Retunrs the sequence for a region in the gene models (exon)
     def chromosome_sequence(region)
@@ -52,11 +52,11 @@
     def add_chromosome_arm(opts)
       @chromosomes = Hash.new unless @chromosomes
       name = opts[:name]
       path = opts[:reference_path]
       path = opts[:alig_path]
-      chromosomes[name] = Bio::DB::Fasta::FastaFile.new(path)
+      chromosomes[name] = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
     end
     
     def add_snp(snp)
       @snp_map[snp.gene] = Array.new unless   @snp_map[snp.gene] 
       @snp_map[snp.gene] << snp
@@ -117,14 +117,15 @@
     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 
+       
           begin 
             file.puts snp.aligned_sequences_fasta
           rescue Exception=>e
             @missing_exons << snp.to_s
-#            $stderr.puts e.to_s
+            $stderr.puts e.to_s
           end
         end
       end
     end
 
\ No newline at end of file