test/test_bfr.rb in bio-polyploid-tools-0.7.3 vs test/test_bfr.rb in bio-polyploid-tools-0.8.0

@@ -1,14 +1,19 @@
+
 $: << File.expand_path(File.dirname(__FILE__) + '/../lib')
 $: << File.expand_path('.')
 path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
 
+tmp_verb = $VERBOSE
+$VERBOSE=nil
 #puts path
 require path
 require 'bio-samtools'
 require "test/unit"
+$VERBOSE=tmp_verb
 
+
 class TestPolyploidTools < Test::Unit::TestCase
 
   
   #Set up the paths
   def setupre
@@ -38,11 +43,11 @@
     setupre
     
     reg="gnl|UG|Ta#S22380157"
     region = @fasta_db.index.region_for_entry(reg).to_region
     min_cov=20
-    puts region.to_s
+    #puts region.to_s
     
     #puts @bam_a.methods
     ref_seq=@fasta_db.fetch_sequence(region)
     reg_a = @bam_a.fetch_region({:region=>region,  :min_cov=>min_cov, :A=>1})
     reg_b = @bam_b.fetch_region({:region=>region,  :min_cov=>min_cov, :A=>1})
@@ -54,31 +59,18 @@
     
     called_1 = reg_a.called
     called_2 = reg_b.called
     
     snps_tot = Bio::Sequence.snps_between(cons_1, cons_2)
-    block_size = 1000
-    snps_per_1k_1   = (block_size * snps_1.to_f   ) / region.size
-    snps_per_1k_2   = (block_size * snps_2.to_f   ) / region.size
-    snps_per_1k_tot = (block_size * snps_tot.to_f ) / region.size
-
-    
-
-    #puts "#{region.entry}\t#{region.size}\t"
-    #puts "#{snps_1}\t#{called_1}\t#{snps_per_1k_1}\t"
-    #puts "#{snps_2}\t#{called_2}\t#{snps_per_1k_2}\t"
-    #puts "#{snps_tot}\t#{snps_per_1k_tot}\n"
-    
-    
+    #block_size = 1000
+    #snps_per_1k_1   = (block_size * snps_1.to_f   ) / region.size
+    #snps_per_1k_2   = (block_size * snps_2.to_f   ) / region.size
+    #snps_per_1k_tot = (block_size * snps_tot.to_f ) / region.size
+        
     snps_tot = Bio::Sequence.snps_between(cons_1, cons_2)
     snps_to_ref = Bio::Sequence.snps_between(cons_1, ref_seq)
-    #puts ">ref\n#{ref_seq}"
-    #puts ">a\n#{cons_1}"
-    #puts ">b\n#{cons_2}"
-    #puts "SNPS between: #{snps_tot}"
-    #puts "SNPS ref: #{snps_to_ref}"
-    #puts "SNPS call: #{snps_to_ref}"
+
     assert_equal(ref_seq.to_s, "acgcttgaccttaggcctatttaggtgacactatagaacaagtttgtacaaaaaagcaggctggtaccggtccggaattcccgggatatcgtcgacccacgcgtccgcgtccgaccagcacaaacaagactgtactctgggctcctctgactccgtgtcttgctaaaatatctttggtcgactcgttgcgaggttgatcagatggcggaggaagcgaagcaggatgtggcgccacccgcgccggagccgaccgaggacgtcgcggacgagaaggtggcggttccgtcgccggaggagtctaaggccctcgttgtcgccgagaatgacgctgagaagcctgcagctacagggggctcacacgaacgagatgctctgctcacgagggtcgcgaccgagaagaggatttcgctgatcaaggcatgggaggagaacgagaaggccaaagccgagaacaaggccgtgaagttgctggcggacatcacctcgtgggagaactccaaggccgcggaactggaagccgagctcaagaagatgcaagagcagctggagaagaagaaggcgcgctgcgtggagaagctcaagaacagcgccgcgacggtgcacaaagaggcggaangagaagcgtgccgcggcggaagcgcggcacggcgaggagatcgtcgcggcggaggagaccgccgccaagtaccgcgccaagggtgaagcgccgaagaagctgctcttcggcagaagatagatatcgcttcatcttcagcttctctctgtttgaccgnttgcatgtctcctgcccatggcatcacttgtgtatttatctttgggggngatcttagtttgtatggtatcatcaaatgcgtcgtga")
     assert_equal(cons_1.to_s , "acgcttgaccttaggcctatttaggtgacactatagaacaagtttgtacaaaaaagcaggctggtaccggtccggaattcccgggatatcgtcgacccacgcgtccgcgtccgaccagcacaaacaagactgtactctgggctcctctgactccgtgtcttgctaaaatatytttggtcgactcgttgcgaggttgatcagatggcggaggaagcgaagcaggatgtggcgccacccgcgccggagccgaccgaggacgtcgcggacgagaaggcggcggttccgtcgccggaggagtctaaggccctsgttgtcgccgagaatgacgcygagaagcctgcagctacagggggctcacacgaacgagatgctctgctcacgagggtygcgaccgagaagaggatttcgctgatcaaggcatgggaggagaaygagaaggccaaagccgagaacaaggccgtgaagttgctggcggacatcacctcgtgggagaactccaaggccgcggaactggaagccgagctcaagaagatgcaagagcagctggagaagaagaaggcgcgctgcgtggagaagctcaagaacagcgccgcgacggtgcacaaagaggcgraaggagaagcgtgccgcggcggaagygcggcrcggcgaggagatcgtcgcggcggaggagaccgccgccaagtaccgcgccaagggtgaggcgccgaagaagctgctcttcggcagaggatagatatcgcttcatcttcagcttctctctgtttgaccgnttgcatgtctcctgcccatggcatcacttgtgtatttatctttgggggngatcttagtttgtatggtatcatcaaatgcgtcgtga")  
     assert_equal(cons_2.to_s , "acgcttgaccttaggcctatttaggtgacactatagaacaagtttgtacaaaaaagcaggctggtaccggtccggaattcccgggatatcgtcgacccacgcgtccgcgtccgaccagcacaaacaagactgtactctgggctcctctgactccgtgtcttgctaaaatatytttggtcgactcgttgcgaggttgatcagatggcggasgaagcgaagcaggatgtggcgccacccgcgccggagccgaccgaggacgtcgcggacgagaaggcggcggttccgtcgccggaggartcyaaggccctsgttgtcgccgagaatgacgcygagaagcctgcagctacagggggctcacacgaacgagatgctctgctcacgagggtygcgaccgagaagaggatttcgctgatcaaggcatgggaggagaaygagaaggccaaagccgagaacaaggccgtgaagttgctggcggacatcacctcgtgggagaactccaaggccgcggaactggaagccgagctcaagaagatgcaagagcagctggagaagaagaaggcgcgctgcgtggagaagctcaagaacagcgccgcgacggtgcacaaagaggcgraaggagaagcgtgccgcggcggaagygcggcgcggcgaggagatcgtcgcggcggaggagrccgccgccaagtaccgcgccaagggtgaggcgccgaagaagctgctcttcggcagaagatagatatcgcttcatcttcagcttctctctgtttgaccgnttgcatgtctcctgcccatggcatcacttgtgtatttatctttgggggngatcttagtttgtatggtatcatcaaatgcgtcgtga")
     assert_equal(snps_tot , 6)
     assert_equal(snps_to_ref , 12)
@@ -106,32 +98,32 @@
     assert_equal(@fasta_db.index.entries.size,1)
     reg = nil
     @fasta_db.index.entries.each do | r |
       i = i  + 1
        
-      reg = container.process_region({:region => r.get_full_region.to_s,:output_file => output_file , :min_cov => 5} )
+      reg = container.process_region({:A => true, :q => 37, :region => r.get_full_region.to_s,:output_file => output_file , :min_cov => 5} )
       #puts reg.inspect
     end
     
     with_bfr = [210, 297, 300, 645, 674]
     
     bases_1 = Array.new
     bases_2 = Array.new
-    bases_1  << {:A=>0, :C=>24, :G=>120, :T=>0}
-    bases_2  << {:A=>0, :C=>24, :G=>112, :T=>0}
-    bases_1  << {:A=>34, :C=>0, :G=>138, :T=>0}
-    bases_2  << {:A=>26, :C=>0, :G=>138, :T=>0}
-    bases_1  << {:A=>0, :C=>32, :G=>0, :T=>141}
-    bases_2  << {:A=>0, :C=>26, :G=>0, :T=>142}
-    bases_1  << {:A=>22, :C=>0, :G=>56, :T=>0}
-    bases_2  << {:A=>62, :C=>0, :G=>25, :T=>0}
-    bases_1  << {:A=>27, :C=>0, :G=>22, :T=>0}
-    bases_2  << {:A=>46, :C=>0, :G=>9, :T=>0}
+    bases_1  << {:A=>0, :C=>24, :G=>147, :T=>0}
+    bases_2  << {:A=>0, :C=>33, :G=>142, :T=>0}
+    bases_1  << {:A=>35, :C=>0, :G=>142, :T=>0}
+    bases_2  << {:A=>25, :C=>0, :G=>149, :T=>0}
+    bases_1  << {:A=>0, :C=>32, :G=>0, :T=>146}
+    bases_2  << {:A=>0, :C=>24, :G=>0, :T=>152}
+    bases_1  << {:A=>22, :C=>0, :G=>38, :T=>0}
+    bases_2  << {:A=>49, :C=>0, :G=>20, :T=>0}
+    bases_1  << {:A=>26, :C=>0, :G=>16, :T=>0}
+    bases_2  << {:A=>36, :C=>0, :G=>10, :T=>0}
     i = 0
     with_bfr.each do | pos |
-      puts pos
-      assert_equal(reg.bases_bulk_1[pos - 1 ] , bases_1[i] )
-      assert_equal(reg.bases_bulk_2[pos - 1 ] , bases_2[i] )
+      #puts pos
+      assert_equal(bases_1[i], reg.bases_bulk_1[pos - 1 ] )
+      assert_equal(bases_2[i], reg.bases_bulk_2[pos - 1 ] )
       i += 1
     end
    
    
     
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