parse_fasta 1.0.1 → 1.1.0

checksums.yaml

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

@@ -18,17 +18,20 @@ Or install it yourself as:
 
 ## Overview ##
 
-I wanted a simple, fast way to parse fasta files so I wouldn't have to
-keep writing annoying boilerplate fasta parsing code everytime I go to
-do something with one. I will probably add more, but likely only tasks
-that I find myself doing over and over.
+I wanted a simple, fast way to parse fasta and fastq files so I
+wouldn't have to keep writing annoying boilerplate parsing code
+everytime I go to do something with a fasta or fastq file. I will
+probably add more, but likely only tasks that I find myself doing over
+and over.
 
-## Usage ##
+## Documentation ##
+
+Checkout [parse_fasta docs](http://rubydoc.info/gems/parse_fasta/1.1.0/frames) to see
+the full documentation.
 
-### Version 1.0.0 (current) ###
+## Usage ##
 
-The monkey patch of the `File` class is no more! Here is the new print
-length example:
+A little script to print header and length of each record.
 
 	require 'parse_fasta'
 
@@ -38,28 +41,37 @@ length example:
 
 And here, a script to calculate GC content:
 
-	require 'parse_fasta'
-
 	FastaFile.open(ARGV.first, 'r').each_record do |header, sequence|
 	  puts [header, sequence.gc].join("\t")
 	end
 
-### Version 0.0.5 (old) ###
+Now we can parse fastq files as well!
 
-An example that lists the length for each sequence. (Won't work in
-version 1.0.0)
+	FastqFile.open(ARGV.first, 'r').each_record do |head, seq, desc, qual|
+	  puts [header, seq, desc, qual.qual_scores.join(',')].join("\t")
+	end
 
-    require 'parse_fasta'
+## Versions ##
 
-	File.open(ARGV.first, 'r').each_record do |header, sequence|
-	  puts [header, sequence.length].join("\t")
-	end
+### 1.1.0 ###
+
+Added: Fastq and Quality classes
+
+### 1.0.0 ###
+
+Added: Fasta and Sequence classes
+
+Removed: File monkey patch
+
+### 0.0.5 ###
+
+Last version with File monkey patch.
 
 ## Benchmark ##
 
-Take these with a grain of salt since `BioRuby` is a heavy weight
+Take these with a grain of salt since `BioRuby` is a big module
 module with lots of features and error checking, whereas `parse_fasta`
-is meant to be lightweight and easy to use for my own coding.
+is meant to be lightweight and easy to use for my own research.
 
 ### FastaFile#each_record ###
 
@@ -78,12 +90,21 @@ was 1.1 gigabytes. Here are the results from Ruby's `Benchmark` class:
 I just wanted a nice, clean way to parse fasta files, but being nearly
 twice as fasta as BioRuby doesn't hurt either!
 
+### FastqFile#each_record ###
+
+The same sequence length test as above, but this time with a fastq
+file containing 4,000,000 illumina reads.
+
+                        user     system      total        real
+    this_fastq     62.610000   1.660000  64.270000 ( 64.389408)
+    bioruby_fastq 165.500000   2.100000 167.600000 (167.969636)
+
 ### Sequence#gc ###
 
 I played around with a few different implementations for the `#gc`
 method and found this one to be the fastest.
 
-The test is done one random strings mating `/[AaCcTtGgUu]/`. `this_gc`
+The test is done on random strings mating `/[AaCcTtGgUu]/`. `this_gc`
 is `Sequence.new(str).gc`, and `bioruby_gc` is
 `Bio::Sequence::NA.new(str).gc_content`.
 

data/lib/parse_fasta/fastq_file.rb

@@ -0,0 +1,65 @@
+# 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/>.
+
+# Provides simple interface for parsing four-line-per-record fastq
+# format files.
+class FastqFile < File
+
+  # Analagous to File#each_line, #each_record is used to go through a
+  # fastq file record by record.
+  #
+  # @example Parsing a fastq file
+  #   FastqFile.open('reads.fq', 'r').each_record do |head, seq, desc, qual|
+  #     # do some fun stuff here!
+  #   end
+  # 
+  # @yield The header, sequence, description and quality string for
+  #   each record in the fastq file to the block
+  # @yieldparam header [String] The header of the fastq record without
+  #   the leading '@'
+  # @yieldparam sequence [Sequence] The sequence of the fastq record
+  # @yieldparam sequence [String] The description line of the fastq
+  #   record without the leading '+'
+  # @yieldparam sequence [Quality] The quality string of the fastq
+  #   record
+  def each_record
+    count = 0
+    header = ''
+    sequence = ''
+    description = ''
+    quality = ''
+    
+    self.each_line do |line|
+      line.chomp!
+
+      case count % 4
+      when 0
+        header = line.sub(/^@/, '')
+      when 1
+        sequence = Sequence.new(line)
+      when 2
+        description = line.sub(/^\+/, '')
+      when 3
+        quality = Quality.new(line)
+        yield(header, sequence, description, quality)
+      end
+      
+      count += 1
+    end
+  end
+end

data/lib/parse_fasta/quality.rb

@@ -0,0 +1,33 @@
+# 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/>.
+
+# Provide some methods for dealing with common tasks regarding
+# quality strings.
+class Quality < String
+
+  # Returns an array of illumina style quality scores. The quality
+  # scores generated will be Phred+33.
+  #
+  # @example Get quality score array of a Quality
+  #   Quality.new("!+5?I").qual_scores #=> [0, 10, 20, 30, 40]
+  #
+  # @return [Array<Fixnum>] the quality scores
+  def qual_scores
+    self.each_byte.map { |b| b - 33 }
+  end
+end

data/lib/parse_fasta/sequence.rb

@@ -19,14 +19,11 @@
 # Provide some methods for dealing with common tasks regarding
 # nucleotide sequences.
 class Sequence < String
-  def initialize(str)
-    super(str)
-  end
 
-  # Returns GC content for self
+  # Calculates GC content
   #
   # Calculates GC content by dividing count of G + C divided by count
-  # of G + C + T + A +U. If there are both T's and U's in the
+  # of G + C + T + A + U. If there are both T's and U's in the
   # Sequence, things will get weird, but then again, that wouldn't
   # happen, now would it!
   #

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 = "1.0.1"
+  VERSION = "1.1.0"
 end

data/lib/parse_fasta.rb

@@ -18,4 +18,6 @@
 
 require 'parse_fasta/version'
 require 'parse_fasta/fasta_file'
+require 'parse_fasta/fastq_file'
 require 'parse_fasta/sequence'
+require 'parse_fasta/quality'

data/parse_fasta.gemspec

@@ -19,8 +19,8 @@ Gem::Specification.new do |spec|
   spec.require_paths = ["lib"]
 
   spec.add_development_dependency "bundler", "~> 1.6"
-  spec.add_development_dependency "rake"
-  spec.add_development_dependency "rspec"
-  spec.add_development_dependency "bio"
-  spec.add_development_dependency "yard"
+  spec.add_development_dependency "rake", "~> 10.3"
+  spec.add_development_dependency "rspec", "~> 2.14"
+  spec.add_development_dependency "bio", "~> 1.4"
+  spec.add_development_dependency "yard", "~> 0.8"
 end

data/spec/lib/fastq_file_spec.rb

@@ -0,0 +1,50 @@
+# 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 FastqFile do
+  describe "#each_record" do
+    let(:fname) { "#{File.dirname(__FILE__)}/../../test_files/test.fq" }
+
+    context "with a 4 line per record fastq file" do
+      before do
+        @records = []
+        FastqFile.open(fname, 'r').each_record do |head, seq, desc, qual|
+          @records << [head, seq, desc, qual]
+        end
+      end
+
+      it "yields the header, sequence, desc, and qual" do
+        expect(@records).to eq([["seq1", "AACCTTGG", "", ")#3gTqN8"],
+                               ["seq2 apples", "ACTG", "seq2 apples",
+                                "*ujM"]])
+      end
+      
+      it "yields the sequence as a Sequence class" do
+        the_sequence = @records[0][1]
+        expect(the_sequence).to be_a(Sequence)
+      end
+
+      it "yields the quality string as a Quality class" do
+        the_quality = @records[0][3]
+        expect(the_quality).to be_a(Quality)
+      end
+    end
+  end
+end

data/spec/lib/quality.rb

@@ -0,0 +1,35 @@
+# 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 Quality do
+  let(:qual_string) { qual_string = Quality.new('ab%63:K') }
+  let(:bioruby_qual_scores) do 
+    Bio::Fastq.new("@seq1\nACTGACT\n+\n#{qual_string}").quality_scores
+  end
+
+  describe "#qual_scores" do
+    context "with illumina style quality scores" do
+      it "returns an array of quality scores" do
+        expect(qual_string.qual_scores).to eq bioruby_qual_scores
+      end
+    end
+  end
+end

data/test_files/benchmark.rb

@@ -54,17 +54,39 @@ 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)
+# 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) }
+# 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
 
-  x.report('this_gc 2') { this_gc(s2) }
-  x.report('bioruby_gc 2') { bioruby_gc(s2) }
+# fastq = ARGV.first
 
-  x.report('this_gc 3') { this_gc(s3) }
-  x.report('bioruby_gc 3') { bioruby_gc(s3) }
+def bioruby_fastq(fastq)
+  Bio::FlatFile.open(Bio::Fastq, fastq) do |fq| 
+    fq.each do |entry| 
+      [entry.definition, entry.seq.length].join("\t")
+    end
+  end
 end
+
+def this_fastq(fastq)
+  FastqFile.open(fastq).each_record do |head, seq, desc, qual|
+    [head, seq.length].join("\t")
+  end
+end
+
+# file is 4 million illumina reads (16,000,000 lines) 1.4gb
+# Benchmark.bmbm do |x|
+#   x.report('this_fastq') { this_fastq(ARGV.first) }
+#   x.report('bioruby_fastq') { bioruby_fastq(ARGV.first) }
+# end

data/test_files/test.fq

@@ -0,0 +1,8 @@
+@seq1
+AACCTTGG
++
+)#3gTqN8
+@seq2 apples
+ACTG
++seq2 apples
+*ujM

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: parse_fasta
 version: !ruby/object:Gem::Version
-  version: 1.0.1
+  version: 1.1.0
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-06-04 00:00:00.000000000 Z
+date: 2014-06-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -28,58 +28,58 @@ dependencies:
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '10.3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '10.3'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '2.14'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '2.14'
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.4'
 - !ruby/object:Gem::Dependency
   name: yard
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.8'
 description: So you want to parse a fasta file...
 email:
 - moorer@udel.edu
@@ -94,14 +94,19 @@ files:
 - Rakefile
 - lib/parse_fasta.rb
 - lib/parse_fasta/fasta_file.rb
+- lib/parse_fasta/fastq_file.rb
+- lib/parse_fasta/quality.rb
 - lib/parse_fasta/sequence.rb
 - lib/parse_fasta/version.rb
 - parse_fasta.gemspec
 - spec/lib/fasta_file_spec.rb
+- spec/lib/fastq_file_spec.rb
+- spec/lib/quality.rb
 - spec/lib/sequence_spec.rb
 - spec/spec_helper.rb
 - test_files/benchmark.rb
 - test_files/test.fa
+- test_files/test.fq
 homepage: https://github.com/mooreryan/parse_fasta
 licenses:
 - 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
@@ -128,6 +133,8 @@ specification_version: 4
 summary: Easy-peasy parsing of fasta files
 test_files:
 - spec/lib/fasta_file_spec.rb
+- spec/lib/fastq_file_spec.rb
+- spec/lib/quality.rb
 - spec/lib/sequence_spec.rb
 - spec/spec_helper.rb
 has_rdoc: