bio-cigar 0.0.1 → 0.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 7882ac6d35a76b43ac78af2218faf7a46a7542eb
+  metadata.gz: 04021bbb9a499a88095d7dbb0da06a82ffbd1cfb
+  data.tar.gz: 2c6cd7124a76a38a6f49e602c007241fde0384f5
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data/VERSION

@@ -1 +1 @@
-0.0.1
+0.1.0

data/lib/bio-cigar/cigar.rb

@@ -13,17 +13,11 @@ module Bio
       ref_index = 0
       query_index = 0
       each_alignment_chunk do |type, count|
+#         puts "ref_i=#{ref_index}, query_index=#{query_index}, num_match=#{num_match}, num_mismatch=#{num_mismatch}"
+#         puts "#{type} #{count}"
+#         puts "ref=#{reference_sequence_string[ref_index...(reference_sequence_string.length)] }"
+#         puts "query=#{query_sequence_string[query_index...(query_sequence_string.length)] }"
         case type
-        when 'M'
-          (0...count).each do |i|
-            if reference_sequence_string[ref_index+i] == query_sequence_string[query_index+i]
-              num_match += 1
-            else
-              num_mismatch += 1
-            end
-          end
-          ref_index += count
-          query_index += count
         when 'I'
           # Extra characters in the query sequence
           num_mismatch += count
@@ -36,12 +30,31 @@ module Bio
           query_index += count
         when 'H'
           query_index += count
+        when 'P'
+          # Do nothing
+        when 'N'
+          # long skip on the reference sequence
+          ref_index += count
         else
-          raise "Cigar string not parsed correctly. Unrecognised alignment type #{type}"
+          if %w(M = X).include?(type)
+            # For = and X, ignore these and recalculate, for ease of programming this method.
+            (0...count).each do |i|
+              if reference_sequence_string[ref_index+i] == query_sequence_string[query_index+i]
+                num_match += 1
+              else
+                num_mismatch += 1
+              end
+            end
+            ref_index += count
+            query_index += count
+          else
+            raise "Cigar string not parsed correctly. Unrecognised alignment type #{type}"
+          end
         end
+        #puts "after, ref_i=#{ref_index}, query_index=#{query_index}, num_match=#{num_match}, num_mismatch=#{num_mismatch}"
       end
 
-      percent = num_match.to_f/(num_match+num_mismatch)*100
+      percent = num_match.to_f / (num_match+num_mismatch)*100
       return percent, num_match, num_mismatch
     end
 
@@ -55,7 +68,7 @@ module Bio
     #    end
     def each_alignment_chunk
       leftover = @cigar_string
-      while matches = leftover.match(/^(\d+)([MSIHD])(.*)/)
+      while matches = leftover.match(/^(\d+)([MSIHNDP\=X])(.*)/)
         yield matches[2], matches[1].to_i
         leftover = matches[3]
       end

data/spec/bio-cigar_spec.rb

@@ -65,4 +65,48 @@ describe "BioCigar" do
     sam.seq = 'TCAGAGCTACAAGAGTTTGATCGTGGCTCAGAAGGAACGCTAGCTATATGCTTAACACATGCAAGTCGAACGTTGTTTTCGGGGAGCTGGGCAGAAGGAAAAGAGGCTCCTAGCGTGAAGGTAGCTTGTCTCGCCCAGGAGGTGGGAACAGTTGAAAACAAAGTGGCGAACGGGTGCGTAATGCGTGGGAATCTGCCGAACAGTTCGGGCCAAATCCTGAAGAAAGCTAAAAAGCGCTGTTTGATGAGCC'
     sam.percent_identity(ref)[0].should == 99.58333333333333
   end
+
+  it 'should work with padded reference seqs' do
+    ref = 'CCGG'
+    sam = Bio::DB::Alignment.new
+    sam.cigar = '2M1P1I1P3I2M'
+    sam.pos = 1
+    sam.seq = 'CCAGGTGG'
+    sam.percent_identity(ref).should == [
+      50.0,
+      4,
+      4,
+      ]
+  end
+
+  it 'should work with X and =' do
+    # SAM:
+    # 790     16      2303416 1150    1       196M54S *       0       0       ACTGCCGGTGTTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGCCCAGGGCTACACACGTGCTACAATGGCCGTTACAAAGCGTCGCTAACCCGCGAGGGGGAGCCAATCGCAAAAAAGCGGCCTCAGTTCAGATTGCAGTCTGCAACTCGACTGCATGAAGTTGGAATCCCTAGTAATCGCGTGTCATTAGCGCGCGGTGAATACGTCCCTGCTCCTTGCACTCACCGCCCGT      *       AS:i:184
+    ref = 'GAGCGAACGTTAGCGGCGGGCTTAACACATGCAAGTCGAACGAGAATGAAGGAGCAATCCTTCTAGTAAAGTGGCGGACGGGTGCGTAACACGTGGATAATCTACCTTCCGGCGGGGGACAACAGTTCGAAAGGACTGCTAATACCGCGTACGTCGGCGAGAGCTCAGGCTCTTGTCGGGAAAGATGGCCAATCCTTGGAAGCTGTCACCGGAAGATGAATCCGCGGCCCATCAGGTAGTTGGTGAGGTAATGGCTCACCAAGCCTAAGACGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGCGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGGCAATGGGCGAAAGCCTGACCCAGCCACGCCGCGTGAGTGATGAAGGCCTTCGGGTCGTAAAGCTCTGTGGGGAGGGACGAACAAGTGCGTATCGAATAAATACGTGCCCTGACGGTACCTCCTTAGCAAGCACCGGCTAACCATGTGCCAGCAGCCGCGGTAATACATGGGGTGCAAACGTTGCTCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTCGCTTAAGTCGGATGTGAAATCCCTCGGCTTAACTGAGGAAGTGCATCCGAGACTGAATGGCTAGAGTACGAAAGAGGGTCGNNNNNTTCCCGGTGTAGAGGTGAAATTCGTAGATATCGGGAGGAACACCGGCGGCGAAGGCGGCGACCTGGTTCGAGACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGGATGCTAGATGTTTCTGGTATTGACCCCGGAGGCGTCGTAGCTAACGCGATAAGCATCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTCAATTTGACGCAACGCGAAGAACCTTACCTGGGTTGGAACCCTCCAGAAGTCCGCAGAGATGTGGATGTGCTCGCAAGAGAACTGGATGTCCAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCGTTAGTTGCTAACAGTTCGGCTGAGCACTCTAACGAGACTGCCGGTGTTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGCCCAGGGCTACACACGTGCTACAATGGTCGTTACAAAGCGTCGCTAACCCGCGAGGGGGAGCTAATCGCAAAAAAGCGGCCTCAGTTCAGATTGCAGTCTGCAACTCGACTGCATGAAGTTGGAATCGCTAGTAATCCCTGATCAGCAGGCAGGGGTGAATACGTTCCCGGGCC'
+    query = 'ACTGCCGGTGTTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGCCCAGGGCTACACACGTGCTACAATGGCCGTTACAAAGCGTCGCTAACCCGCGAGGGGGAGCCAATCGCAAAAAAGCGGCCTCAGTTCAGATTGCAGTCTGCAACTCGACTGCATGAAGTTGGAATCCCTAGTAATCGCGTGTCATTAGCGCGCGGTGAATACGTCCCTGCTCCTTGCACTCACCGCCCGT'
+    pos = 1150
+
+    ref_seq = ref[pos-1...ref.length]
+    Bio::Cigar.new('100X96=54S').percent_identity(ref_seq, query).should == [ #This example is a little fake because X and = are not true, but it is re-calculated in the code so should not matter
+      98.46938775510205,
+      193,
+      3
+    ]
+  end
+
+  it 'should work with N' do
+    ref =   'GTGTCGCCCGTCTAGCATACGCATGATCGACTGTCAGCTAGTCAGACTA'
+    query = 'GTGTAACCC'+                             'TCAGAATA'
+    sam = Bio::DB::Alignment.new
+    sam.cigar = '9M32N8M'
+    sam.pos = 1
+    sam.seq = query
+    expected_matches = 4+3+4+3
+    expected_mismatches = 2+1
+    sam.percent_identity(ref).should == [
+      expected_matches.to_f/ (expected_matches+expected_mismatches)*100,
+      expected_matches,
+      expected_mismatches,
+      ]
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-cigar
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.1.0
 platform: ruby
 authors:
 - Ben J Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-02-27 00:00:00.000000000 Z
+date: 2014-02-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-samtools