parse_fasta 1.5.2 → 1.6.0

checksums.yaml

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data/.coveralls.yml

@@ -0,0 +1 @@
+service_name: travis-ci

data/.travis.yml

@@ -0,0 +1,18 @@
+language: ruby
+cache: bundler
+
+rvm:
+  - 1.9.3
+  - 2.0
+  - 2.1
+  - 2.2.0
+  - 2.2.2
+
+script: 'bundle exec rake'
+
+notifications:
+  email:
+    recipients:
+      - moorer@udel.edu
+    on_failure: change
+    on_success: never

data/README.md

@@ -1,6 +1,6 @@
 # parse_fasta #
 
-[![Gem Version](https://badge.fury.io/rb/parse_fasta.svg)](http://badge.fury.io/rb/parse_fasta)
+[![Gem Version](https://badge.fury.io/rb/parse_fasta.svg)](http://badge.fury.io/rb/parse_fasta) [![Build Status](https://travis-ci.org/mooreryan/parse_fasta.svg?branch=master)](https://travis-ci.org/mooreryan/parse_fasta) [![Coverage Status](https://coveralls.io/repos/mooreryan/parse_fasta/badge.svg)](https://coveralls.io/r/mooreryan/parse_fasta)
 
 So you want to parse a fasta file...
 
@@ -20,17 +20,15 @@ Or install it yourself as:
 
 ## Overview ##
 
-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.
+Provides nice, programmatic access to fasta and fastq files, as well
+as providing Sequence and Quality helper classes. It's more
+lightweight than BioRuby. And more fun! ;)
 
 ## Documentation ##
 
 Checkout
-[parse_fasta docs](http://rubydoc.info/gems/parse_fasta/1.5.0/frames)
-to see the full documentation.
+[parse_fasta docs](http://rubydoc.info/gems/parse_fasta/1.6.0/frames)
+for the full api documentation.
 
 ## Usage ##
 
@@ -40,36 +38,51 @@ A little script to print header and length of each record.
 
 	require 'parse_fasta'
 
-	FastaFile.open(ARGV.first, 'r').each_record do |header, sequence|
+	FastaFile.open(ARGV[0]).each_record do |header, sequence|
 	  puts [header, sequence.length].join("\t")
 	end
 
 And here, a script to calculate GC content:
 
-	FastaFile.open(ARGV.first, 'r').each_record do |header, sequence|
+	FastaFile.open(ARGV[0]).each_record do |header, sequence|
 	  puts [header, sequence.gc].join("\t")
 	end
 
 Now we can parse fastq files as well!
 
-	FastqFile.open(ARGV.first, 'r').each_record do |head, seq, desc, qual|
-	  puts [header, seq, desc, qual.qual_scores.join(',')].join("\t")
+	FastqFile.open(ARGV[0]).each_record do |head, seq, desc, qual|
+	  puts [header, qual.qual_scores.join(',')].join("\t")
+	end
+
+What if you don't care if the input is a fastA or a fastQ? No problem!
+
+	SeqFile.open(ARGV[0]).each_record do |head, seq|
+	  puts [header, seq].join "\t"
 	end
 
 ## Versions ##
 
-### 1.5.0 ###
+### 1.6 ###
+
+Added `SeqFile` class, which accepts either fastA or fastQ files. It
+uses FastaFile and FastqFile internally. You can use this class if you
+want your scripts to accept either fastA or fastQ files.
+
+If you need the description and quality string, you should use
+FastqFile instead.
+
+### 1.5 ###
 
 Now accepts gzipped files. Huzzah!
 
-### 1.4.0 ###
+### 1.4 ###
 
 Added methods:
 
     Sequence.base_counts
 	Sequence.base_frequencies
 
-### 1.3.0 ###
+### 1.3 ###
 
 Add additional functionality to `each_record` method.
 
@@ -108,7 +121,7 @@ Then info will contain the following arrays
 	['fruits', ['pineapple', 'pear', 'peach']],
 	['veggies', ['peppers', 'parsnip', 'peas']]
 
-### 1.2.0 ###
+### 1.2 ###
 
 Added `mean_qual` method to the `Quality` class.
 
@@ -119,11 +132,11 @@ Dropped Ruby requirement to 1.9.3
 (Note, if you want to build the docs with yard and you're using
 Ruby 1.9.3, you may have to install the redcarpet gem.)
 
-### 1.1.0 ###
+### 1.1 ###
 
 Added: Fastq and Quality classes
 
-### 1.0.0 ###
+### 1.0 ###
 
 Added: Fasta and Sequence classes
 
@@ -135,16 +148,17 @@ Last version with File monkey patch.
 
 ## Benchmark ##
 
-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 research.
+Perhaps this isn't exactly fair since `BioRuby` is a big module with
+lots of features and error checking, whereas `parse_fasta` is meant to
+be lightweight and easy to use for my own research. Oh well ;)
 
 ### FastaFile#each_record ###
 
-Just for fun, I wanted to compare the execution time to that of
-BioRuby. I calculated sequence length for each fasta record with both
-the `each_record` method from this gem and using the `FastaFormat`
-class from BioRuby. You can see the test script in `benchmark.rb`.
+You're probably wondering...How does it compare to BioRuby in some
+super accurate benchmarking tests? Lucky for you, I calculated
+sequence length for each fasta record with both the `each_record`
+method from this gem and using the `FastaFormat` class from
+BioRuby. You can see the test script in `benchmark.rb`.
 
 The test file contained 2,009,897 illumina reads and the file size
 was 1.1 gigabytes. Here are the results from Ruby's `Benchmark` class:
@@ -153,8 +167,7 @@ was 1.1 gigabytes. Here are the results from Ruby's `Benchmark` class:
     parse_fasta  64.530000   1.740000  66.270000 ( 67.081502)
     bioruby     116.250000   2.260000 118.510000 (120.223710)
 
-I just wanted a nice, clean way to parse fasta files, but being nearly
-twice as fasta as BioRuby doesn't hurt either!
+Hot dog! It's faster :)
 
 ### FastqFile#each_record ###
 
@@ -167,14 +180,11 @@ file containing 4,000,000 illumina reads.
 
 ### 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 on random strings mating `/[AaCcTtGgUu]/`. `this_gc`
+The test is done on random strings matcing `/[AaCcTtGgUu]/`. `this_gc`
 is `Sequence.new(str).gc`, and `bioruby_gc` is
 `Bio::Sequence::NA.new(str).gc_content`.
 
-To see how the methods scale, the test 1 string was 2,000,000 bases,
+To see how the methods scales, the test 1 string was 2,000,000 bases,
 test 2 was 4,000,000 and test 3 was 8,000,000 bases.
 
                        user     system      total        real
@@ -189,7 +199,21 @@ test 2 was 4,000,000 and test 3 was 8,000,000 bases.
 
 Nice!
 
+Troll: "But Ryan, when will you find the GC of an 8,000,000 base
+sequence?"
+
+Me: "Step off, troll!"
+
+## Test suite & docs ##
+
+For a good time, you could clone this repo and run the test suite with
+rspec! Or if you just don't trust that it works like it should. The
+specs probably need a little clean up...so fork it and clean it up ;)
+
+Same with the docs. Clone the repo and build them yourself with `yard`
+if you are in need of some excitement.
+
 ## Notes ##
 
-Currently in doesn't check whether your file is actually a fasta file
-or anything, so watch out.
+Only the `SeqFile` class actually checks to make sure that you passed
+in a "proper" fastA or fastQ file, so watch out.

data/lib/parse_fasta/seq_file.rb

@@ -0,0 +1,82 @@
+# Copyright 2014, 2015 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 a class that will parse either fastA or fastQ files,
+# depending on what the user provides. Handles, gzipped files.
+class SeqFile < File
+
+  # Analagous to IO#each_line, #each_record will go through a fastA or
+  # fastQ file record by record.
+  #
+  # This #each_record is used in a similar fashion as
+  # FastaFile#each_record except that it yields the header and the
+  # sequence regardless of whether the input is a fastA file or a
+  # fastQ file.
+  #
+  # If the input is a fastQ file, this method will yield the header
+  # and the sequence and ignore the description and the quality
+  # string. This SeqFile class should only be used if your program
+  # needs to work on either fastA or fastQ files, thus it ignores the
+  # quality string and description and treats either file type as if
+  # it were a fastA file.
+  #
+  # If you need the description or quality, you should use
+  # FastqFile#each_record instead.
+  #
+  # @example Parse a gzipped fastA file
+  #   SeqFile.open('reads.fa.gz').each_record do |head, seq|
+  #     puts [head, seq.length].join "\t"
+  #   end
+  #
+  # @example Parse an uncompressed fastQ file
+  #   SeqFile.open('reads.fq.gz').each_record do |head, seq|
+  #     puts [head, seq.length].join "\t"
+  #   end
+  #
+  # @yieldparam header [String] The header of the record without the
+  #   leading '>' or '@'
+  #
+  # @yieldparam sequence [Sequence] The sequence of the record.
+  def each_record
+    first_char = get_first_char(self)
+    
+    if first_char == '>'
+      FastaFile.open(self).each_record do |header, sequence|
+        yield(header, sequence)
+      end
+    elsif first_char == '@'
+      FastqFile.open(self).each_record do |head, seq, desc, qual|
+        yield(head, seq)
+      end
+    else
+      raise ArgumentError, "Input does not look like FASTA or FASTQ"
+    end      
+  end
+
+  private
+
+  def get_first_char(f)
+    begin
+      handle = Zlib::GzipReader.open(f)
+    rescue Zlib::GzipFile::Error => e
+      handle = f
+    end      
+
+    handle.each_line.peek[0]
+  end
+end

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 = "1.5.2"
+  VERSION = "1.6.0"
 end

data/lib/parse_fasta.rb

@@ -19,5 +19,6 @@
 require 'parse_fasta/version'
 require 'parse_fasta/fasta_file'
 require 'parse_fasta/fastq_file'
+require 'parse_fasta/seq_file'
 require 'parse_fasta/sequence'
 require 'parse_fasta/quality'

data/parse_fasta.gemspec

@@ -28,4 +28,5 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency "rspec", "~> 2.14"
   spec.add_development_dependency "bio", "~> 1.4"
   spec.add_development_dependency "yard", "~> 0.8"
+  spec.add_development_dependency "coveralls", "~> 0.7"
 end

data/spec/lib/seq_file_spec.rb

@@ -0,0 +1,150 @@
+# Copyright 2014, 2015 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 SeqFile do
+  describe "#each_record" do
+    let(:records) {
+      [["seq1 is fun", "AACTGGNNN"],
+       ["seq2", "AATCCTGNNN"],
+       ["seq3", "yyyyyyyyyyyyyyyNNN"]]
+    }
+
+    context "when input is a fasta file" do
+      let(:f_handle) { SeqFile.open(@fname).each_record { |s| } }
+      
+      shared_examples_for "parsing a fasta file" do
+        it "yields proper header and sequence for each record" do
+          expect { |b|
+            SeqFile.open(@fname).each_record(&b)
+          }.to yield_successive_args(*records)
+        end
+
+        it "yields the sequence as a Sequence class" do
+          SeqFile.open(@fname).each_record do |_, seq|
+            expect(seq).to be_an_instance_of Sequence
+          end
+        end
+      end
+
+      context "with a gzipped file" do
+        before(:each) do
+          @fname = "#{File.dirname(__FILE__)}/../../test_files/test.fa.gz"
+        end
+
+        it_behaves_like "parsing a fasta file"
+
+        it "closes the GzipReader" do
+          expect(f_handle).to be_closed
+        end
+
+        it "returns GzipReader object" do
+          expect(f_handle).to be_an_instance_of Zlib::GzipReader
+        end
+      end
+
+      context "with a non-gzipped file" do
+        before(:each) do
+          @fname = "#{File.dirname(__FILE__)}/../../test_files/test.fa"
+        end
+
+        it_behaves_like "parsing a fasta file"
+
+        it "doesn't close the File (approx regular file behavior)" do
+          expect(f_handle).not_to be_closed
+        end
+
+        it "returns FastaFile object" do
+          expect(f_handle).to be_a FastaFile
+        end
+      end
+    end
+  end
+
+  context "when input is a fastq file" do
+    let(:records) {
+      [["seq1", "AACCTTGG"],
+       ["seq2 apples", "ACTG"]] }
+    let(:f_handle) { SeqFile.open(@fname).each_record { |s| } }
+
+    shared_examples_for "parsing a fastq file" do
+      it "yields only header & sequence" do
+        expect { |b|
+          SeqFile.open(@fname).each_record(&b)
+        }.to yield_successive_args(records[0], records[1])
+      end
+
+      it "yields the sequence as a Sequence class" do
+        SeqFile.open(@fname).each_record do |_, seq, _, _|
+          expect(seq).to be_an_instance_of Sequence
+        end
+      end
+    end
+    
+    context "with a 4 line per record fastq file" do
+      describe "#each_record" do
+        context "with a gzipped file" do
+          before(:each) do
+            @fname =
+              "#{File.dirname(__FILE__)}/../../test_files/test.fq.gz"
+          end
+
+          it_behaves_like "parsing a fastq file"
+
+          it "closes the GzipReader" do
+            expect(f_handle).to be_closed
+          end
+
+          it "returns GzipReader object" do
+            expect(f_handle).to be_an_instance_of Zlib::GzipReader
+          end
+        end
+
+        context "with a non-gzipped file" do
+          before(:each) do
+            @fname =
+              "#{File.dirname(__FILE__)}/../../test_files/test.fq"
+          end
+
+          it_behaves_like "parsing a fastq file"
+
+          it "doesn't close the SeqFile (approx reg file behav)" do
+            expect(f_handle).not_to be_closed
+          end
+
+          it "returns FastqFile object" do
+            expect(f_handle).to be_a FastqFile
+          end
+        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"
+
+      expect { SeqFile.open(fname).each_record do |h, s|
+          puts [h, s].join ' '
+        end
+      }.to raise_error(ArgumentError, err_msg)
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -16,4 +16,8 @@
 # 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 'coveralls'
+Coveralls.wear!
+
 require 'parse_fasta'
+

data/test_files/bogus.txt

@@ -0,0 +1,2 @@
+this header is missing the '>'
+ACTGACTGATCGATCGTAGCTACGTAGCTACG

data/test_files/test.fa

@@ -1,8 +1,10 @@
 >seq1 is fun
 AACTGGNNN
+
 >seq2
 AAT
 CCTGNNN
+
 >seq3
 yyyyyyyyyy
 

metadata

@@ -1,85 +1,99 @@
 --- !ruby/object:Gem::Specification
 name: parse_fasta
 version: !ruby/object:Gem::Version
-  version: 1.5.2
+  version: 1.6.0
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-01-08 00:00:00.000000000 Z
+date: 2015-04-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.6'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.6'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '10.3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '10.3'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.14'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.14'
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.4'
 - !ruby/object:Gem::Dependency
   name: yard
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
 description: Provides nice, programmatic access to fasta and fastq files, as well
   as providing Sequence and Quality helper classes. No need for BioRuby ;)
 email:
@@ -88,7 +102,9 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
-- .gitignore
+- ".coveralls.yml"
+- ".gitignore"
+- ".travis.yml"
 - COPYING
 - Gemfile
 - README.md
@@ -97,22 +113,25 @@ files:
 - lib/parse_fasta/fasta_file.rb
 - lib/parse_fasta/fastq_file.rb
 - lib/parse_fasta/quality.rb
+- lib/parse_fasta/seq_file.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_spec.rb
+- spec/lib/seq_file_spec.rb
 - spec/lib/sequence_spec.rb
 - spec/spec_helper.rb
 - test_files/benchmark.rb
+- test_files/bogus.txt
 - test_files/test.fa
 - test_files/test.fa.gz
 - test_files/test.fq
 - test_files/test.fq.gz
 homepage: https://github.com/mooreryan/parse_fasta
 licenses:
-- ! 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
+- 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
 metadata: {}
 post_install_message: 
 rdoc_options: []
@@ -120,17 +139,17 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: 1.9.3
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 2.4.6
 signing_key: 
 specification_version: 4
 summary: Easy-peasy parsing of fasta & fastq files!
@@ -138,6 +157,7 @@ test_files:
 - spec/lib/fasta_file_spec.rb
 - spec/lib/fastq_file_spec.rb
 - spec/lib/quality_spec.rb
+- spec/lib/seq_file_spec.rb
 - spec/lib/sequence_spec.rb
 - spec/spec_helper.rb
 has_rdoc: