bin/polymarker.rb in bio-polyploid-tools-0.3.1 vs bin/polymarker.rb in bio-polyploid-tools-0.3.3

@@ -8,19 +8,35 @@
 $: << File.expand_path(File.dirname(__FILE__) + '/../lib')
 $: << File.expand_path('.')
 path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
 require path
 
+arm_selection_functions = Hash.new;
 
 
+arm_selection_functions[:arm_selection_first_two] = lambda do | contig_name |
+  ret = contig_name[0,2]       
+  return ret
+end
+#Function to parse stuff like: IWGSC_CSS_1AL_scaff_110
+arm_selection_functions[:arm_selection_embl] = lambda do | contig_name|
+  ret = contig_name.split('_')[2][0,2]
+  return ret
+end
 
+arm_selection_functions[:arm_selection_morex] = lambda do | contig_name |
+  ret = contig_name.split(':')[0].split("_")[1];       
+  return ret
+end
+
 options = {}
 options[:path_to_contigs] = "/tgac/references/external/projects/iwgsc/css/IWGSC_CSS_all_scaff_v1.fa"
 options[:chunks] = 1
 options[:bucket_size] = 0
 options[:bucket] = 1
 options[:model] = "est2genome"
+options[:arm_selection] = arm_selection_functions[:arm_selection_embl] ;
 OptionParser.new do |opts|
   opts.banner = "Usage: polymarker.rb [options]"
 
   opts.on("-c", "--contigs FILE", "File with contigs to use as database") do |o|
     options[:path_to_contigs] = o
@@ -43,10 +59,14 @@
   end
   
   opts.on("-e", "--exonerate_model MODEL", "Model to be used in exonerate to search for the contigs") do |o|
      options[:model] = o
    end
+
+   opts.on("-a", "--arm_selection arm_selection_embl|arm_selection_morex|arm_selection_first_two", "Function to decide the chromome arm") do |o|
+    options[:arm_selection] = arm_selection_functions[o.to_sym];
+   end
   
     
 end.parse!
 
 p options
@@ -113,12 +133,18 @@
     snp = nil
     if options[:marker_list] #List with Sequence
       snp = Bio::PolyploidTools::SNPSequence.parse(line)  
     elsif options[:snp_list] and options[:reference] #List and fasta file
       snp = Bio::PolyploidTools::SNP.parse(line)
-      region = fasta_reference_db.index.region_for_entry(snp.gene).get_full_region
-      snp.template_sequence = fasta_reference_db.fetch_sequence(region)
+      entry = fasta_reference_db.index.region_for_entry(snp.gene)
+      if entry
+       region = fasta_reference_db.index.region_for_entry(snp.gene).get_full_region
+       snp.template_sequence = fasta_reference_db.fetch_sequence(region)
+     else
+        $stderr.puts "Unable to find entry for #{snp.gene}"
+      end
+
     else
       rise Bio::DB::Exonerate::ExonerateException.new "Wrong number of arguments. " 
     end
     rise Bio::DB::Exonerate::ExonerateException.new "No SNP for line '#{line}'" if snp == nil
     snp.snp_in = snp_in
@@ -176,20 +202,12 @@
 
 #4. Load all the results from exonerate and get the input filename for primer3
 #Custom arm selection function that only uses the first two characters. Maybe
 #we want to make it a bit more cleaver
 write_status "Reading best alignment on each chromosome"
-arm_selection_first_two = lambda do | contig_name |
-  ret = contig_name[0,2]       
-  return ret
-end
-#Function to parse stuff like: IWGSC_CSS_1AL_scaff_110
-arm_selection_embl = lambda do | contig_name|
-  ret = contig_name.split('_')[2][0,2]
-  return ret
-end
 
+
 container= Bio::PolyploidTools::ExonContainer.new
 container.flanking_size=100
 container.gene_models(temp_fasta_query)
 container.chromosomes(temp_contigs)
 container.add_parental({:name=>snp_in})
@@ -197,10 +215,10 @@
 snps.each do |snp|
   snp.container = container
   snp.flanking_size = container.flanking_size
   container.add_snp(snp)
 end
-container.add_alignments({:exonerate_file=>exonerate_file, :arm_selection=>arm_selection_embl, :min_identity=>min_identity})
+container.add_alignments({:exonerate_file=>exonerate_file, :arm_selection=>options[:arm_selection] , :min_identity=>min_identity})
 
 
 #4.1 generating primer3 file
 write_status "Running primer3"
 file = File.open(exons_filename, "w")
\ No newline at end of file