parse_fasta 2.4.1 → 2.4.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 902fe63af8592d8cbc0a1e78d251e365f5344f0b
+  metadata.gz: c235357c072f2b4042b7723dd0c3eb686d5fc60d
+  data.tar.gz: 7f1d7ba7d306774fe35b79f9ec6f773265e7c93e
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+  data.tar.gz: 8d7bee5a8f0cf74db20616165dd0d00a4caa44eec7701e1a4a48ddf6349a6906aa05033307de01b05af8eb5b2fb5e96d7818058c744527ce5ec6cf68a7f1c6d8

data/lib/parse_fasta/core_ext/string.rb

@@ -8,6 +8,7 @@ module ParseFasta
       #   # First inclued the methods
       #   String.include ParseFasta::CoreExt::String
       #
+      #   # The default gap char is '-'
       #   "--A-C-t-g".remove_gaps #=> "ACtg"
       #
       # @example Change the gap character to 'n'
@@ -16,11 +17,28 @@ module ParseFasta
       #
       #   "-N-nACTG".remove_gaps "N" #=> "--nACTG"
       #
-      # @param gap_char [String] the character to treat as a gap
+      # @example Passing multiple gap chars
+      #   # First inclued the methods
+      #   String.include ParseFasta::CoreExt::String
+      #
+      #   ".A----C_t~~~~g^G3".remove_gaps '^._-~3' #=> "ACtgG"
+      #
+      # @param gap_char [String] the character(s) to treat as a gap
       #
       # @return [String] a string with all instances of
       #   gap_char_removed
       def remove_gaps gap_char="-"
+
+        if gap_char.length > 1
+          if gap_char.include? "^"
+            gap_char.sub! '^', '\\^'
+          end
+
+          if gap_char.include? "-"
+            gap_char.sub! '-', '\\-'
+          end
+        end
+
         self.tr gap_char, ""
       end
     end

data/lib/parse_fasta/version.rb

@@ -1,3 +1,3 @@
 module ParseFasta
-  VERSION = "2.4.1"
+  VERSION = "2.4.2"
 end

data/spec/parse_fasta/core_ext/string_spec.rb

@@ -26,6 +26,14 @@ module ParseFasta
 
           expect(aln.remove_gaps "N").to eq expected
         end
+
+        it "can handle multiple weird gap chars" do
+          # The '-' and '^' chars are treated specially by String#tr.
+          aln = ".A----C_t~~~~g^G3"
+          expected = "ACtgG"
+
+          expect(aln.remove_gaps '^._-~3').to eq expected
+        end
       end
     end
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: parse_fasta
 version: !ruby/object:Gem::Version
-  version: 2.4.1
+  version: 2.4.2
 platform: ruby
 authors:
 - Ryan Moore