parse_fasta 2.1.1 → 2.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -1,5 +1,9 @@
 ## Versions ##
 
+### 2.2.0 ###
+
+Add `id` attribute to `Record`.
+
 ### 2.1.1 ###
 
 Speed up `Record.new`

data/lib/parse_fasta/record.rb

@@ -22,6 +22,9 @@ module ParseFasta
     # @!attribute header
     #   @return [String] the full header of the record without the '>'
     #     or '@'
+    # @!attribute id
+    #   @return [String] the "id" i.e., the first token when split by
+    #     whitespace
     # @!attribute seq
     #   @return [String] the sequence of the record
     # @!attribute desc
@@ -30,7 +33,7 @@ module ParseFasta
     # @!attribute qual
     #   @return [String or Nil] if the record is from a fastA file, it
     #     is nil; else, the quality string of the fastQ record
-    attr_accessor :header, :seq, :desc, :qual
+    attr_accessor :header, :id, :seq, :desc, :qual
 
     # The constructor takes keyword args.
     #
@@ -48,6 +51,7 @@ module ParseFasta
     #   character in it
     def initialize args = {}
       @header = args.fetch :header
+      @id = @header.split(" ")[0]
 
       @desc = args.fetch :desc, nil
       @qual = args.fetch :qual, nil

data/lib/parse_fasta/version.rb

@@ -17,5 +17,5 @@
 # along with parse_fasta.  If not, see <http://www.gnu.org/licenses/>.
 
 module ParseFasta
-  VERSION = "2.1.1"
+  VERSION = "2.2.0"
 end

data/spec/parse_fasta/record_spec.rb

@@ -21,8 +21,9 @@ require "spec_helper"
 module ParseFasta
   describe Record do
     let(:header)  { "apple pie is good"}
+    let(:id)      { "apple" }
     let(:seq)     { "ACTG" }
-    let(:desc) { "apple" }
+    let(:desc)    { "apple" }
     let(:qual)    { "abcd" }
 
     let(:fasta_rec) {
@@ -37,15 +38,31 @@ module ParseFasta
     }
 
     describe "::new" do
-      context "fastA input" do
+      context "either fastA or fastQ" do
         it "sets :header" do
           expect(fasta_rec.header).to eq header
+          expect(fastq_rec.header).to eq header
         end
 
         it "sets :seq" do
           expect(fasta_rec.seq).to eq seq
+          expect(fastq_rec.seq).to eq seq
+        end
+
+        it "sets :id" do
+          expect(fasta_rec.id).to eq id
+          expect(fastq_rec.id).to eq id
         end
 
+        it "sets :id to the first token when split by whitespace" do
+          rec = Record.new header: "apple\tpie is good",
+                           seq: "actg"
+
+          expect(rec.id).to eq "apple"
+        end
+      end
+
+      context "fastA input" do
         it "sets :desc to nil" do
           expect(fasta_rec.desc).to eq nil
         end
@@ -65,19 +82,11 @@ module ParseFasta
       end
 
       context "fastQ input" do
-        it "sets :header" do
-          expect(fastq_rec.header).to eq header
-        end
-
-        it "sets :seq" do
-          expect(fastq_rec.seq).to eq seq
-        end
-
-        it "sets :desc to nil" do
+        it "sets :desc to desc" do
           expect(fastq_rec.desc).to eq desc
         end
 
-        it "sets :qual to nil" do
+        it "sets :qual to qual" do
           expect(fastq_rec.qual).to eq qual
         end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: parse_fasta
 version: !ruby/object:Gem::Version
-  version: 2.1.1
+  version: 2.2.0
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-11-01 00:00:00.000000000 Z
+date: 2016-11-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler