Bug fix: parse error when unaligned regions exist

 * Bug fix: parse error when unaligned regions exist. Thanks to
   Tomoaki NISHIYAMA who reports the bug ([BioRuby] SIM4 parser).
 * To confirm the bug fix, tests are added with new test data.

lib/bio/appl/sim4/report.rb

@@ -161,7 +161,7 @@ def initialize(seq1, seq2, midline = nil,
         attr_reader :percent_identity
 
         # Returns directions of mapping.
-        # Maybe one of "->", "<-" or "" or nil.
+        # Maybe one of "->", "<-", "==" or "" or nil.
         # This would be a Bio::Sim4 specific method.
         attr_reader :direction
 
@@ -170,7 +170,7 @@ def initialize(seq1, seq2, midline = nil,
         # Bio::Sim4::Report::Hit class.
         # Users shall not use it directly.
         def self.parse(str, aln)
-          /^(\d+)\-(\d+)\s*\((\d+)\-(\d+)\)\s*([\d\.]+)\%\s*([\-\<\>]*)/ =~ str
+          /^(\d+)\-(\d+)\s*\((\d+)\-(\d+)\)\s*([\d\.]+)\%\s*([\-\<\>\=]*)/ =~ str
           self.new(Segment.new($1, $2, aln[0]),
                    Segment.new($3, $4, aln[2]),
                    aln[1], $5, $6)
@@ -198,6 +198,17 @@ def self.seq2_intron(prev_e, e, aln)
                    aln[1])
         end
 
+        # Parses part of sim4 result text and creates a new SegmentPair
+        # object for regions which can not be aligned correctly.
+        # It is designed to be called internally from
+        # Bio::Sim4::Report::Hit class.
+        # Users shall not use it directly.
+        def self.both_intron(prev_e, e, aln)
+          self.new(Segment.new(prev_e.seq1.to+1, e.seq1.from-1, aln[0]),
+                   Segment.new(prev_e.seq2.to+1, e.seq2.from-1, aln[2]),
+                   aln[1])
+        end
+
         #--
         # Bio::BLAST::*::Report::Hsp compatible methods
         #   Methods already defined: midline, percent_identity
@@ -318,7 +329,9 @@ def parse_segmentpairs
             exo << e
             if ai then
               # intron data in alignment
-              if ai[2].strip.empty? then
+              if ai[1].strip.empty? then
+                i = SegmentPair.both_intron(prev_e, e, ai)
+              elsif ai[2].strip.empty? then
                 i = SegmentPair.seq1_intron(prev_e, e, ai)
               else
                 i = SegmentPair.seq2_intron(prev_e, e, ai)
@@ -338,11 +351,24 @@ def parse_segmentpairs
         # Parses alignment.
         def parse_align
           s1 = []; ml = []; s2 = []
+          blocks = []
+          blocks.push [ s1, ml, s2 ]
           dat = @data[1..-1]
           return unless dat
           dat.each do |str|
             a = str.split(/\r?\n/)
-            a.shift
+            ruler = a.shift
+            # First line, for example,
+            # "     50     .    :    .    :    .    :    .    :    .    :"
+            # When the number is 0, forced to be a separated block
+            if /^\s*(\d+)/ =~ ruler and $1.to_i == 0 and !ml.empty? then
+              s1 = []; ml = []; s2 = []
+              blocks.push [ s1, ml, s2 ]
+            end
+            # For example,
+            # "    190 GAGTCATGCATGATACAA          CTTATATATGTACTTAGCGGCA"
+            # "        ||||||||||||||||||<<<...<<<-||-|||||||||||||||||||"
+            # "    400 GAGTCATGCATGATACAACTT...AGCGCT ATATATGTACTTAGCGGCA"
             if /^(\s*\d+\s)(.+)$/ =~ a[0] then
               range = ($1.length)..($1.length + $2.chomp.length - 1)
               a.collect! { |x| x[range] }
@@ -351,16 +377,23 @@ def parse_align
               s2 << a.shift
             end
           end #each
-          alx  = ml.join('').split(/([\<\>]+\.+[\<\>]+)/)
-          seq1 = s1.join(''); seq2 = s2.join('')
-          i = 0
-          alx.collect! do |x|
-            len = x.length
-            y = [ seq1[i, len], x, seq2[i, len] ]
-            i += len
-            y
+          alx_all = []
+          blocks.each do |ary|
+            s1, ml, s2 = ary
+            alx  = ml.join('').split(/([\<\>]+\.+[\<\>]+)/)
+            seq1 = s1.join(''); seq2 = s2.join('')
+            i = 0
+            alx.collect! do |x|
+              len = x.length
+              y = [ seq1[i, len], x, seq2[i, len] ]
+              i += len
+              y
+            end
+            # adds virtual intron information if necessary
+            alx_all.push([ '', '', '' ]) unless alx_all.empty?
+            alx_all.concat alx
           end
-          @align = alx
+          @align = alx_all
         end
         private :parse_align
 

test/data/sim4/complement-A4.sim4

@@ -0,0 +1,43 @@
+
+seq1 = sample41-1c.fst, 284 bp
+seq2 = sample40-2.fst (genome4), 770 bp
+
+>mrna4c
+>genome4
+
+(complement)
+
+1-72  (351-424)   89% ->
+73-142  (563-630)   95% ==
+213-284  (700-770)   95%
+
+      0     .    :    .    :    .    :    .    :    .    :
+      1 TTTTAGCCGGCACGAGATTG AGCGTATGATCACGCGCGCGGCCTCCT C
+        ||||||||||||||||||||-||||-||||||||||||||||||||||-|
+    351 TTTTAGCCGGCACGAGATTGCAGCG ATGATCACGCGCGCGGCCTCCTAC
+
+     50     .    :    .    :    .    :    .    :    .    :
+     49 AGAGTGATGCATGATACAACTT AT          ATATGTACTTAGCTG
+        -|||| ||||||||||||||||- |->>>...>>>|||||||||||||-|
+    400  GAGTCATGCATGATACAACTTCTTGGTT...GATATATGTACTTAGC G
+
+    100     .    :    .    :    .    :    .    :    .    :
+     88 GCAACCGAGATTTACTTTCGAAGCACTGTGATGAACCCGCGGCCCTTTGA
+        ||||||||||||||||||||||| |||||||||||||||||-||||||||
+    577 GCAACCGAGATTTACTTTCGAAGGACTGTGATGAACCCGCG CCCTTTGA
+
+    150     .
+    138 GCGCT
+        |||||
+    626 GCGCT
+
+      0     .    :    .    :    .    :    .    :    .    :
+    213 TATATATGTACTTAGCGG ACACCGAGATTTACTTTCGAAGGACTGTGGA
+        ||||||||||||||||||-|-|||||||||||||||||||||||||||-|
+    700 TATATATGTACTTAGCGGCA ACCGAGATTTACTTTCGAAGGACTGTG A
+
+     50     .    :    .    :
+    262 TGAACCCGCGCCCTTTGAGCGCT
+        |||||||||||||||||||||||
+    748 TGAACCCGCGCCCTTTGAGCGCT
+