parse_fasta 1.6.1 → 1.6.2

checksums.yaml

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

@@ -27,7 +27,7 @@ lightweight than BioRuby. And more fun! ;)
 ## Documentation ##
 
 Checkout
-[parse_fasta docs](http://rubydoc.info/gems/parse_fasta/1.6.0/frames)
+[parse_fasta docs](http://rubydoc.info/gems/parse_fasta/1.6.2/frames)
 for the full api documentation.
 
 ## Usage ##
@@ -76,6 +76,11 @@ FastqFile instead.
 Better internal handling of empty sequences -- instead of raising
 errors, pass empty sequences.
 
+#### 1.6.2 ####
+
+`FastaFile::open` now raises a `ParseFasta::DataFormatError` when passed files
+that don't begin with a `>`.
+
 ### 1.5 ###
 
 Now accepts gzipped files. Huzzah!

data/lib/parse_fasta/fasta_file.rb

@@ -22,6 +22,27 @@ require 'zlib'
 # files are no problem.
 class FastaFile < File
 
+  # Use it like IO::open
+  #
+  # @param fname [String] the name of the file to open
+  #
+  # @return [FastaFile] a FastaFile
+  def self.open(fname, *args)
+    begin
+      handle = Zlib::GzipReader.open(fname)
+    rescue Zlib::GzipFile::Error => e
+      handle = File.open(fname)
+    end
+
+    unless handle.each_char.peek[0] == '>'
+      raise ParseFasta::DataFormatError
+    end
+
+    handle.close
+
+    super
+  end
+
   # Analagous to IO#each_line, #each_record is used to go through a
   # fasta file record by record. It will accept gzipped files as well.
   #

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 = "1.6.1"
+  VERSION = "1.6.2"
 end

data/lib/parse_fasta.rb

@@ -22,3 +22,12 @@ require 'parse_fasta/fastq_file'
 require 'parse_fasta/seq_file'
 require 'parse_fasta/sequence'
 require 'parse_fasta/quality'
+
+module ParseFasta
+  # Error raised when FASTA file is malformed
+  class DataFormatError < IOError
+    def message
+      "lalala"
+    end
+  end
+end

data/spec/lib/fasta_file_spec.rb

@@ -19,6 +19,31 @@
 require 'spec_helper'
 
 describe FastaFile do
+  describe "::open" do
+    context "when input is bogus" do
+      it "raises a ParseFasta::DataFormatError with message" do
+        fname = "#{File.dirname(__FILE__)}/../../test_files/bogus.txt"
+
+        expect { FastaFile.open(fname).each_record do |h, s|
+            puts [h, s].join ' '
+          end
+        }.to raise_error ParseFasta::DataFormatError
+      end
+    end
+
+    let(:fasta) { "#{File.dirname(__FILE__)}/../../test_files/test.fa" }
+
+    it "takes all the wacky args like IO.open" do
+      expect {
+        FastaFile.open(fasta, mode: 'r', cr_newline: true)
+      }.not_to raise_error
+    end
+
+    it "returns a FastaFile" do
+      expect(FastaFile.open(fasta)).to be_a FastaFile
+    end
+  end
+
   describe "#each_record" do
     let(:records) { Helpers::RECORDS }
 

data/spec/lib/seq_file_spec.rb

@@ -131,17 +131,17 @@ describe SeqFile do
         end
       end
     end
-  end
 
-  context "when input is bogus" do
-    it "raises an ArgumentError with message" do
-      fname = "#{File.dirname(__FILE__)}/../../test_files/bogus.txt"
-      err_msg = "Input does not look like FASTA or FASTQ"
+    context "when input is bogus" do
+      it "raises an ArgumentError with message" do
+        fname = "#{File.dirname(__FILE__)}/../../test_files/bogus.txt"
+        err_msg = "Input does not look like FASTA or FASTQ"
 
-      expect { SeqFile.open(fname).each_record do |h, s|
-          puts [h, s].join ' '
-        end
-      }.to raise_error(ArgumentError, err_msg)
+        expect { SeqFile.open(fname).each_record do |h, s|
+            puts [h, s].join ' '
+          end
+        }.to raise_error(ArgumentError, err_msg)
+      end
     end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: parse_fasta
 version: !ruby/object:Gem::Version
-  version: 1.6.1
+  version: 1.6.2
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-05-11 00:00:00.000000000 Z
+date: 2015-05-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler