parse_fasta 0.0.5 → 1.0.0

data/spec/lib/fasta_file_spec.rb

@@ -0,0 +1,46 @@
+# Copyright 2014 Ryan Moore
+# Contact: moorer@udel.edu
+#
+# This file is part of parse_fasta.
+#
+# parse_fasta is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# parse_fasta is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with parse_fasta.  If not, see <http://www.gnu.org/licenses/>.
+
+require 'spec_helper'
+
+describe FastaFile do
+  describe "#each_record" do
+
+    let(:fname) { "#{File.dirname(__FILE__)}/../../test_files/test.fa" }
+    it "yields a block with header and sequence for each record in a fasta file" do
+      seqs = []
+      FastaFile.open(fname, 'r').each_record do |header, sequence|
+        seqs << [header, sequence]
+      end
+      
+      expect(seqs).to eq([["seq1 is fun", "AACTGGend"],
+                          ["seq2", "AATCCTGend"],
+                          ["seq3", "yyyyyyyyyyyyyyyend"]])
+
+    end
+
+    it "passes header of type string as first parameter" do
+      sequence_class = nil
+      FastaFile.open(fname, 'r').each_record do |header, sequence|
+        sequence_class = sequence.class
+        break
+      end
+      expect(sequence_class).to be Sequence
+    end      
+  end
+end

data/spec/lib/sequence_spec.rb

@@ -0,0 +1,52 @@
+# Copyright 2014 Ryan Moore
+# Contact: moorer@udel.edu
+#
+# This file is part of parse_fasta.
+#
+# parse_fasta is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# parse_fasta is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with parse_fasta.  If not, see <http://www.gnu.org/licenses/>.
+
+require 'spec_helper'
+require 'bio'
+
+describe Sequence do
+  describe "#gc" do
+
+    it "gives the same answer as BioRuby" do
+      s = 'ACtgcGAtcgCgAaTtGgCcnNuU'
+      bioruby_gc = Bio::Sequence::NA.new(s).gc_content
+      expect(Sequence.new(s).gc).to eq bioruby_gc
+    end
+
+    context "when sequence isn't empty" do
+      it "calculates gc" do
+        s = Sequence.new('ActGnu')
+        expect(s.gc).to eq(2 / 5.to_f)
+      end
+    end
+
+    context "when sequence is empty" do
+      it "returns 0" do
+        s = Sequence.new('')
+        expect(s.gc).to eq 0
+      end
+    end
+
+    context "there are no A, C, T, G or U (ie only N)" do
+      it "returns 0" do
+        s = Sequence.new('NNNNNnn')
+        expect(s.gc).to eq 0
+      end
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,19 @@
+# Copyright 2014 Ryan Moore
+# Contact: moorer@udel.edu
+#
+# This file is part of parse_fasta.
+#
+# parse_fasta is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# parse_fasta is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with parse_fasta.  If not, see <http://www.gnu.org/licenses/>.
+
+require 'parse_fasta'

data/test_files/benchmark.rb

@@ -0,0 +1,70 @@
+#!/usr/bin/env ruby
+
+# Copyright 2014 Ryan Moore
+# Contact: moorer@udel.edu
+
+# This file is part of parse_fasta.
+
+# parse_fasta is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+# parse_fasta is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with parse_fasta.  If not, see <http://www.gnu.org/licenses/>.
+
+require 'parse_fasta'
+require 'bio'
+require 'benchmark'
+
+def this_parse_fasta fname
+  FastaFile.open(fname, 'r').each_record do |header, sequence|
+    [header, sequence.length].join("\t")
+  end
+end
+
+def bioruby_parse_fasta fname
+  Bio::FastaFormat.open(fname).each do |entry|
+    [entry.definition, entry.seq.length].join("\t")
+  end
+end
+
+# Benchmark.bmbm do |x|
+#   x.report('parse_fasta') { this_parse_fasta(ARGV.first) }
+#   x.report('bioruby')     { bioruby_parse_fasta(ARGV.first) }
+# end
+
+####
+
+def this_gc(str)
+  Sequence.new(str).gc
+end
+
+def bioruby_gc(str)
+  Bio::Sequence::NA.new(str).gc_content
+end
+
+# make a random sequence of given length
+def make_seq(num)
+  num.times.reduce('') { |str, n| str << %w[A a C c T t G g N n].sample }
+end
+
+s1 = make_seq(2000000)
+s2 = make_seq(4000000)
+s3 = make_seq(8000000)
+
+Benchmark.bmbm do |x|
+  x.report('this_gc 1') { this_gc(s1) }
+  x.report('bioruby_gc 1') { bioruby_gc(s1) }
+
+  x.report('this_gc 2') { this_gc(s2) }
+  x.report('bioruby_gc 2') { bioruby_gc(s2) }
+
+  x.report('this_gc 3') { this_gc(s3) }
+  x.report('bioruby_gc 3') { bioruby_gc(s3) }
+end

data/test_files/test.fa

@@ -0,0 +1,9 @@
+>seq1 is fun
+AACTGGend
+>seq2
+AAT
+CCTGend
+>seq3
+yyyyyyyyyy
+yyyyy
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: parse_fasta
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: 1.0.0
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-31 00:00:00.000000000 Z
+date: 2014-06-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -38,6 +38,48 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 description: So you want to parse a fasta file...
 email:
 - moorer@udel.edu
@@ -46,14 +88,38 @@ extensions: []
 extra_rdoc_files: []
 files:
 - ".gitignore"
+- COPYING
 - Gemfile
-- LICENSE.txt
 - README.md
 - Rakefile
-- benchmark.rb
+- doc/FastaFile.html
+- doc/File.html
+- doc/ParseFasta.html
+- doc/Sequence.html
+- doc/_index.html
+- doc/class_list.html
+- doc/css/common.css
+- doc/css/full_list.css
+- doc/css/style.css
+- doc/file.README.html
+- doc/file_list.html
+- doc/frames.html
+- doc/index.html
+- doc/js/app.js
+- doc/js/full_list.js
+- doc/js/jquery.js
+- doc/method_list.html
+- doc/top-level-namespace.html
 - lib/parse_fasta.rb
+- lib/parse_fasta/fasta_file.rb
+- lib/parse_fasta/sequence.rb
 - lib/parse_fasta/version.rb
 - parse_fasta.gemspec
+- spec/lib/fasta_file_spec.rb
+- spec/lib/sequence_spec.rb
+- spec/spec_helper.rb
+- test_files/benchmark.rb
+- test_files/test.fa
 homepage: https://github.com/mooreryan/parse_fasta
 licenses:
 - 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
@@ -78,4 +144,8 @@ rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: Easy-peasy parsing of fasta files
-test_files: []
+test_files:
+- spec/lib/fasta_file_spec.rb
+- spec/lib/sequence_spec.rb
+- spec/spec_helper.rb
+has_rdoc: 

data/LICENSE.txt

@@ -1,22 +0,0 @@
-Copyright (c) 2014 Ryan Moore
-
-MIT License
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/benchmark.rb

@@ -1,22 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'parse_fasta'
-require 'bio'
-require 'benchmark'
-
-def parse_fasta fname
-  File.open(fname, 'r').each_record do |header, sequence|
-    [header, sequence.length].join("\t")
-  end
-end
-
-def bioruby fname
-  Bio::FastaFormat.open(fname).each do |entry|
-    [entry.definition, entry.seq.length].join("\t")
-  end
-end
-
-Benchmark.bmbm do |x|
-  x.report('parse_fasta') { parse_fasta(ARGV.first) }
-  x.report('bioruby')     { bioruby(ARGV.first) }
-end