now parsing all locations except two (technically non-standard) ones

cjfields · Sep 11, 2014 · 840c581 · 840c581
1 parent dd324ba
commit 840c581
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Showing 2 changed files with 26 additions and 25 deletions.
diff --git a/lib/Bio/Tools/FTLocationParser.pm6 b/lib/Bio/Tools/FTLocationParser.pm6
@@ -40,15 +40,18 @@ grammar Bio::Grammar::Location {
     token functional_operator { 'join' | 'order' | 'complement' }
 
     #base_position ::= <integer> | <low_base_bound> | <high_base_bound> |  <two_base_bound> 
-    token base_position { <abs_base_position> | <low_base_bound> | <high_base_bound> |  <two_base_bound> }
+    token base_position { <abs_base_position> | <low_base_bound> | <high_base_bound> |  <uncertain_bound> | <two_base_bound> }
 
     # my addition
     token abs_base_position { \d+ }
 
     # low_base_bound ::= > <integer>
     token low_base_bound { '>' <abs_base_position> }
+
     token high_base_bound { '<' <abs_base_position> }
 
+    token uncertain_bound { '?' <abs_base_position>? }
+
     # two_base_bound ::= <base_position>.<base_position>
     token two_base_bound { '('? <abs_base_position>'.'<abs_base_position> ')'? }
 

diff --git a/t/Tools/FTLocationParser.t b/t/Tools/FTLocationParser.t
@@ -41,27 +41,27 @@ my %testcases =
     #     122, 133, "WITHIN", 204, 221, "WITHIN", "EXACT", 0, 1, Nil],
 
     # UNCERTAIN locations and positions (Swissprot)
-    #"?2465..2774" => [0,
-    #    2465, 2465, "UNCERTAIN", 2774, 2774, "EXACT", "EXACT", 0, 1, Nil],
-    #"22..?64" => [0,
-    #    22, 22, "EXACT", 64, 64, "UNCERTAIN", "EXACT", 0, 1, Nil],
-    #"?22..?64" => [0,
-    #    22, 22, "UNCERTAIN", 64, 64, "UNCERTAIN", "EXACT", 0, 1, Nil],
-    #"?..>393" => [0,
-    #    Nil, Nil, "UNCERTAIN", 393, Nil, "AFTER", "EXACT", 0, 1, Nil],
-    #"<1..?" => [0,
-    #    Nil, 1, "BEFORE", Nil, Nil, "UNCERTAIN", "EXACT", 0, 1, Nil],
-    #"?..536" => [0,
-    #    Nil, Nil, "UNCERTAIN", 536, 536, "EXACT", "EXACT", 0, 1, Nil],
-    #"1..?" => [0,
-    #    1, 1, "EXACT", Nil, Nil, "UNCERTAIN", "EXACT", 0, 1, Nil],
-    #"?..?" => [0,
-    #    Nil, Nil, "UNCERTAIN", Nil, Nil, "UNCERTAIN", "EXACT", 0, 1, Nil],
-    #"1..?12" => [0,
-    #    1, 1, "EXACT", 12, 12, "UNCERTAIN", "EXACT", 0, 1, Nil],
-    ## Not sure if this is legal...
-    #"?" => [0,
-    #    Nil, Nil, "UNCERTAIN", Nil, Nil, "EXACT", "EXACT", 0, 1, Nil],
+    "?2465..2774" => [0,
+        2465, 2465, "UNCERTAIN", 2774, 2774, "EXACT", "EXACT", 0, 1, Nil],
+    "22..?64" => [0,
+        22, 22, "EXACT", 64, 64, "UNCERTAIN", "EXACT", 0, 1, Nil],
+    "?22..?64" => [0,
+        22, 22, "UNCERTAIN", 64, 64, "UNCERTAIN", "EXACT", 0, 1, Nil],
+    "?..>393" => [0,
+        Nil, Nil, "UNCERTAIN", 393, Nil, "AFTER", "EXACT", 0, 1, Nil],
+    "<1..?" => [0,
+        Nil, 1, "BEFORE", Nil, Nil, "UNCERTAIN", "EXACT", 0, 1, Nil],
+    "?..536" => [0,
+        Nil, Nil, "UNCERTAIN", 536, 536, "EXACT", "EXACT", 0, 1, Nil],
+    "1..?" => [0,
+        1, 1, "EXACT", Nil, Nil, "UNCERTAIN", "EXACT", 0, 1, Nil],
+    "?..?" => [0,
+        Nil, Nil, "UNCERTAIN", Nil, Nil, "UNCERTAIN", "EXACT", 0, 1, Nil],
+    "1..?12" => [0,
+        1, 1, "EXACT", 12, 12, "UNCERTAIN", "EXACT", 0, 1, Nil],
+    # Not sure if this is legal...
+    "?" => [0,
+        Nil, Nil, "UNCERTAIN", Nil, Nil, "EXACT", "EXACT", 0, 1, Nil],
 
     # Split locations (now collections of locations)
 
@@ -123,9 +123,7 @@ for %testcases.keys -> $locstr {
 
     Bio::Grammar::Location.parse($locstr);
 
-    say "$locstr" if !$/.defined;
-    say $/.gist;
-
+    ok($/.defined, $locstr);
 }
 
 done();