parse_fasta 2.1.0 → 2.1.1

checksums.yaml

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

@@ -1,5 +1,9 @@
 ## Versions ##
 
+### 2.1.1 ###
+
+Speed up `Record.new`
+
 ### 2.1.0 ###
 
 Add `#to_s`, `#to_fasta`, and `#to_fastq` to `Record`.

data/README.md

@@ -62,7 +62,7 @@ ParseFasta::SeqFile.open(ARGV[0]).each_record do |rec|
     # it's a fastQ record
   else
     # it's a fastA record
-  end  
+  end
 end
 ```
 
@@ -74,7 +74,7 @@ ParseFasta::SeqFile.open(ARGV[0]).each_record do |rec|
     # it's a fastQ record
   else
     # it's a fastA record
-  end  
+  end
 end
 ```
 
@@ -85,3 +85,11 @@ ParseFasta::SeqFile.open(ARGV[0]).each_record do |rec|
   puts rec.to_s
 end
 ```
+
+But of course, since it is a `#to_s` override...you don't even have to call it directly!
+
+```ruby
+ParseFasta::SeqFile.open(ARGV[0]).each_record do |rec|
+  puts rec
+end
+```

data/lib/parse_fasta/record.rb

@@ -52,9 +52,10 @@ module ParseFasta
       @desc = args.fetch :desc, nil
       @qual = args.fetch :qual, nil
 
-      @qual.gsub!(/\s+/, "") if @qual
+      @qual.tr!(" \t\n\r", "") if @qual
 
-      seq = args.fetch(:seq).gsub(/\s+/, "")
+      seq = args.fetch(:seq)
+      seq.tr!(" \t\n\r", "")
 
       if fastq? # is fastQ
         @seq = seq
@@ -163,7 +164,7 @@ module ParseFasta
     private
 
     def check_fasta_seq seq
-      if seq.match ">"
+      if seq.include? ">"
         raise ParseFasta::Error::SequenceFormatError,
               "A sequence contained a '>' character " +
                   "(the fastA file record separator)"

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 = "2.1.0"
+  VERSION = "2.1.1"
 end

data/spec/parse_fasta/record_spec.rb

@@ -27,11 +27,11 @@ module ParseFasta
 
     let(:fasta_rec) {
       Record.new header: header,
-                 seq:    "A C\t\t   T   G\r"
+                 seq:    "A \r\n\r\n\tC\t\t \n  T   G\r"
     }
     let(:fastq_rec) {
       Record.new header: header,
-                 seq:    "A C\t\t   T   G\r",
+                 seq:    "A \r\n\r\n\tC\t\t \n  T   G\r",
                  desc:   desc,
                  qual:   " a  b \tcd "
     }

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: parse_fasta
 version: !ruby/object:Gem::Version
-  version: 2.1.0
+  version: 2.1.1
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-10-22 00:00:00.000000000 Z
+date: 2016-11-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler