parse_fasta 0.0.4 → 0.0.5

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data/.gitignore

@@ -0,0 +1,22 @@
+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+*.bundle
+*.so
+*.o
+*.a
+mkmf.log

data/Gemfile

@@ -0,0 +1,4 @@
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in parse_fasta.gemspec
+gemspec

data/LICENSE.txt

@@ -0,0 +1,22 @@
+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/README.md

@@ -0,0 +1,58 @@
+# parse_fasta #
+
+So you want to parse a fasta file...
+
+## Installation ##
+
+Add this line to your application's Gemfile:
+
+    gem 'parse_fasta'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install parse_fasta
+
+## Overview ##
+
+Provides the method `#each_record` for the `File` class.
+
+	each_record { |header, sequence| block }
+
+The whole file is not loaded into memory, so have no fear of giant
+fasta files!
+
+## Usage ##
+
+An example that lists the length for each sequence.
+
+    require 'parse_fasta'
+
+	File.open(ARGV.first, 'r').each_record do |header, sequence|
+	  puts [header, sequence.length].join("\t")
+	end
+
+## Benchmark ##
+
+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`.
+
+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:
+
+                      user     system      total        real
+    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!
+
+## Notes ##
+
+Currently in doesn't check whether your file is actually a fasta file
+or anything, so watch out.

data/Rakefile

@@ -0,0 +1,2 @@
+require "bundler/gem_tasks"
+

data/benchmark.rb

@@ -0,0 +1,22 @@
+#!/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

data/lib/parse_fasta/version.rb

@@ -0,0 +1,3 @@
+module ParseFasta
+  VERSION = "0.0.5"
+end

data/lib/parse_fasta.rb

@@ -1,4 +1,5 @@
 # Copyright 2014 Ryan Moore
+# Contact: moorer@udel.edu
 
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -13,6 +14,8 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+require "parse_fasta/version"
+
 class File
   def each_record
     self.each("\n>") do |line|

data/parse_fasta.gemspec

@@ -0,0 +1,23 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'parse_fasta/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "parse_fasta"
+  spec.version       = ParseFasta::VERSION
+  spec.authors       = ["Ryan Moore"]
+  spec.email         = ["moorer@udel.edu"]
+  spec.summary       = %q{Easy-peasy parsing of fasta files}
+  spec.description   = %q{So you want to parse a fasta file...}
+  spec.homepage      = "https://github.com/mooreryan/parse_fasta"
+  spec.license       = "GPLv3: http://www.gnu.org/licenses/gpl.txt"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.6"
+  spec.add_development_dependency "rake"
+end

metadata

@@ -1,25 +1,62 @@
 --- !ruby/object:Gem::Specification
 name: parse_fasta
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.0.5
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-30 00:00:00.000000000 Z
-dependencies: []
-description: A simple extension of the File class to easily parse fasta files.
-email: moorer@udel.edu
+date: 2014-05-31 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: '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
 executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- benchmark.rb
 - lib/parse_fasta.rb
+- lib/parse_fasta/version.rb
+- parse_fasta.gemspec
 homepage: https://github.com/mooreryan/parse_fasta
 licenses:
-- http://www.gnu.org/licenses/gpl.txt
+- 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
 metadata: {}
 post_install_message: 
 rdoc_options: []
@@ -40,5 +77,5 @@ rubyforge_project:
 rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
-summary: Simple API for parsing fasta files
+summary: Easy-peasy parsing of fasta files
 test_files: []