ABIF 0.0.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 8209086fa0fd89bb8c512306fbb483b238265a20
+  data.tar.gz: e439aefb5b8f8d864365fdbd94a29ed8c6d5d422
+SHA512:
+  metadata.gz: ca2ff2b3f0a162039a130d691093508540d1d3eb66050a5e99e35f419b1d270c2ceca5f894fa6d7e04246d42adec0aef8f84b92d635a4040e8a0ca1be849ac94
+  data.tar.gz: f3041d14381c0aae42617f1e2cc2a724b427392cdd65cfc33640e281f47e2515bf27e9a1e91bd99be3207c893f88d2e9f119d1e74f026e1ac9e28400e91eb963

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+.DS_Store

data/ABIF.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'ABIF/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "ABIF"
+  spec.version       = ABIF::VERSION
+  spec.authors       = ["Sascha Willuweit"]
+  spec.email         = ["s@rprojekt.org"]
+  spec.description   = %q{ABIF file format reader/parse/plotter.}
+  spec.summary       = %q{Handle/Parse/Plot ABIF (Applied Biosystems Genetic Analysis Data File Format) FSA, AB1 and HID files.}
+  spec.homepage      = "https://github.com/545ch4/ABIF"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  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_dependency "thor"
+
+  spec.add_development_dependency "bundler", "~> 1.3"
+  spec.add_development_dependency "minitest"
+  spec.add_development_dependency "rake"
+end

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in ABIF.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2013 Sascha Willuweit
+
+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

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+# ABIF
+
+Handle ABIF (Applied Biosystems Genetic Analysis Data File Format) FSA, AB1 and HID files.
+
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'ABIF'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install ABIF
+
+
+## Usage
+
+file = ABIF::File.new(<.fsa|ab1|hid file or IO stream>)
+puts file.data.keys
+puts file.data['RunN_1']
+
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+#!/usr/bin/env rake
+require "bundler/gem_tasks"
+ 
+require 'rake/testtask'
+ 
+Rake::TestTask.new do |t|
+  t.libs << 'lib/ABIF'
+  t.test_files = FileList['test/lib/ABIF/*_test.rb']
+  t.verbose = true
+end
+ 
+task :default => :test

data/bin/abifcli

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+#!/usr/bin/env ruby
+require 'ABIF/CLI'
+ABIF::CLI.start

data/lib/ABIF.rb

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+require "ABIF/version"
+require "ABIF/file"
+# This program is a ABIF file (Applied Biosystems Genetic Analysis Data File Format)
+# reader. It takes a ABIF file (.fsa) or HID file (.hid) and reading its content to several arrays of (named) datapoints.
+# For in-depths description of the file format see http://www.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf
+#
+# Author::    Sascha Willuweit  (s@rprojekt.org)
+# Copyright:: Copyright (c) 2013 Sascha Willuweit
+# License::   CreativeCommons Attribution-NonCommercial-ShareAlike 3.0 Unported License (see http://creativecommons.org/licenses/by-nc-sa/3.0/)
+module ABIF
+end

data/lib/ABIF/cli.rb

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+require 'thor'
+require 'tempfile'
+require 'open3'
+require 'abif'
+
+module ABIF
+	class CLI < Thor
+		class_option :verbose, :type => :boolean
+		class_option :version, :type => :boolean
+
+		desc "test FILE", "Test validity of FILE"
+		def test(filename)
+			print_version if options[:version]
+			puts ABIF::File.supported? filename, options.select{|option| [].include? option}
+		end
+
+		option :format, :type => :string, :default => 'dat'
+		option :normalize, :type => :string, :default => 'none'
+		desc "parse FILE", "parse FILE "
+		def parse(filename)
+			print_version if options[:version]
+
+			f = ABIF::File.new filename, options.select{|option| [:normalize].include? option}
+			refrence_datapoints = f.data['DATA_1'].size
+			channels = f.data.keys.select{|channel| channel.include?('DATA_') && f.data[channel].size == refrence_datapoints}
+			case options[:format]
+			when 'csv'
+				puts "index," << channels.join(",")
+				refrence_datapoints.times do |i|
+				puts "#{i}," << channels.map{|channel| f.data[channel][i]}.join(",")
+				end
+			when 'raw'
+				f.data.each do |key, d|
+					puts "#{key} (#{f.data_params[key].join(',')}): #{d.inspect}"
+				end
+			else
+				puts "index\t" << channels.join("\t")
+				refrence_datapoints.times do |i|
+				puts "#{i}\t" << channels.map{|channel| f.data[channel][i]}.join("\t")
+				end
+			end
+			exit 0
+		end
+
+		option :format, :type => :string, :default => 'png'
+		option :size, :type => :string, :default => '5000,6000'
+		option :normalize, :type => :string, :default => 'none'
+		desc "plot FILE OUTFILE", "plot FILE into OUTFILE"
+		def plot(filename, outfilename)
+			print_version if options[:version]
+
+			#colors = ['blue', 'green', 'black', 'red', 'orange', 'purple']
+
+			f = ABIF::File.new filename, options.select{|option| [:normalize].include? option}
+			tmpfile = Tempfile.new('abifcli.dat')
+
+			refrence_datapoints = f.data['DATA_1'].size
+			channels = f.data.keys.select{|channel| channel.include?('DATA_') && f.data[channel].size == refrence_datapoints}
+			tmpfile.puts "index\t" << channels.join("\t")
+			refrence_datapoints.times do |i|
+				tmpfile.puts "#{i}\t" << channels.map{|channel| f.data[channel][i]}.join("\t")
+			end
+			tmpfile.close
+
+			IO.popen(%w{gnuplot}, 'r+') do |gnuplot|
+				gnuplot.puts "set terminal #{options[:format].inspect} size #{options[:size]}"
+				gnuplot.puts "set output #{outfilename.inspect}"
+				gnuplot.puts "set multiplot layout #{channels.size}, 1 title #{filename.inspect}"
+				channels.each_with_index.map do |channel, i|
+					gnuplot.puts "set title #{channel.inspect}"
+					gnuplot.puts "unset key"
+					gnuplot.puts "plot #{tmpfile.path.inspect} using 1:#{i + 2} with lines lt 1 lc rgb 'grey' lw 1"
+				end
+				gnuplot.puts "unset multiplot"
+				gnuplot.puts "exit"
+				gnuplot.close_write
+			end
+
+			tmpfile.unlink
+
+			exit 0
+		end
+	
+	private
+	
+		def print_version
+			puts "abifcli version #{ABIF::VERSION}"
+			exit 0
+		end
+	end
+end

data/lib/ABIF/file.rb

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+require 'zlib'
+require 'openssl'
+
+module ABIF
+	# This class holds the FSA/HID file format data. It's initialized given the filename or an IO object.
+	# Options are:
+	# [:normalize] All channels are normalized with respect to their 500-datapoint-tail assuming it means-up to 0.
+	class File
+		attr_reader :filetype, :fileversion, :data, :data_params
+
+		def self.supported?(filename_or_io, options = {})
+			ft = nil
+			fv = 0
+			begin
+				io = filename_or_io.respond_to?(:seek) ? filename_or_io : ::File.open(filename_or_io, 'rb')
+				(ft, fv) = io.read(6).unpack('A4S>')
+			rescue Exception => e
+				raise IOError.new "Error reding ABIF file: #{e}"
+			ensure
+				io.close unless io.nil? || !io.respond_to?(:close)
+			end
+			return ft == 'ABIF' && fv >= 100
+		end
+
+		def initialize(filename_or_io, options = {})
+			@data = {}
+			@data_params = {}
+			@named_data = {}
+			@some_counter = 1
+
+			@decipher = OpenSSL::Cipher.new('DES-CBC')
+			@decipher.key = "W\xB6\xBF\xBC\xFE\xBA1&" # [87, -74, -65, -68, -2, -70, 49, 38].pack('c*')
+			@decipher.iv = "\x8E\x129\x9C\aroZ" # [-114, 18, 57, -100, 7, 114, 111, 90].pack('c*')
+
+			io = nil
+			begin
+				io = filename_or_io.respond_to?(:seek) ? filename_or_io : ::File.open(filename_or_io, 'rb')
+				(@filetype, @fileversion) = io.read(6).unpack('A4S>')
+				raise IOError.new('Not an ABIF file') unless @filetype == 'ABIF' && @fileversion >= 100
+				header_dir_entry = unpack_dir_entry(io)
+				io.seek(header_dir_entry[:data_offset])
+				header_dir_entry[:num_elements].times do
+					dir_entry = unpack_dir_entry(io)
+					old_pos = io.pos
+					if dir_entry[:element_size] * dir_entry[:num_elements] > 4
+						io.seek(dir_entry[:data_offset])
+					else
+						io.seek(-8, IO::SEEK_CUR)
+					end
+
+					@data_params["#{dir_entry[:name]}_#{dir_entry[:number]}"] = [dir_entry[:element_type], dir_entry[:element_size], dir_entry[:num_elements], dir_entry[:data_size]]
+					@data["#{dir_entry[:name]}_#{dir_entry[:number]}"] = unpack_data(dir_entry[:element_type], dir_entry[:element_size], dir_entry[:num_elements], dir_entry[:data_size], io)
+					io.seek(old_pos)
+				end
+			rescue Exception => e
+				raise IOError.new "Error reding ABIF file: #{e}"
+			ensure
+				io.close unless io.nil? || !io.respond_to?(:close)
+			end
+
+			if options[:normalize] && options[:normalize] != 'none'
+				data_length = @data['DATA_1'].size
+				@data.keys.select{|key| key.include?('DATA_') && @data[key].size == data_length}.each do |key|
+					mean = 0.0
+					if options[:normalize] == 'head'
+						mean = @data[key][500..(500+[499,data_length].min)].inject(0.0){|t, datapoint| t + datapoint} / [499,data_length].min.to_f
+					elsif options[:normalize] == 'tail'
+						mean = @data[key][-500..-1].inject(0.0){|t, datapoint| t + datapoint} / 500.0
+					end
+					@data[key] = @data[key].map{|i| i - mean}
+				end
+			end
+		end
+
+	private
+
+		def some_counter
+			@some_counter = @some_counter + 1
+		end
+
+		def unpack_dir_entry(io)
+			dir_entry = {}
+			dir_entry[:name], dir_entry[:number], dir_entry[:element_type], dir_entry[:element_size], dir_entry[:num_elements], dir_entry[:data_size], dir_entry[:data_offset], dir_entry[:data_handle] = io.read(28).unpack('A4L>S>S>L>L>L>L>')
+			dir_entry
+		end
+
+		def unpack_data(type, size, num, data_size, io)
+			# TODO Checksum
+			#   Fields: CkSm, CkSm-1, CkSm-2, CLst
+			#   split by ':' 
+			#   Objects: java.util.Collections.synchronizedSortedSet/java.util.SortedSet/TreeSet/java.util.SortedSet
+			# 	MD5 BASE64Encoder "ABIFAdmin", "IdeABu++inghedsmiteCLI4S3", "81tingpH!sh1es", "eleMENT5ConsOLI45Dated", "AloysiusANdauGUST1NE"
+			data = io.read(data_size)
+			case type
+			when 0 # IllegalType -1-byte(s) wide
+				"illegal type 'IllegalType'(#{type})"
+			when 1 # Byte 1-byte(s) wide
+				data.unpack('C' * num)
+			when 2 # Char 1-byte(s) wide
+				data.unpack('C' * num)
+			when 3 # Word 2-byte(s) wide
+				data.unpack('S>' * num)
+			when 4 # Short 2-byte(s) wide
+				data.unpack('s>' * num)
+			when 5 # Long 4-byte(s) wide
+				data.unpack('l>' * num)
+			when 6 # Rational 8-byte(s) wide
+				struct = {}
+				struct[:numerator], struct[:denumerator] = data.unpack('l>l>' * num)
+				struct
+			when 7 # Float 4-byte(s) wide
+				data.unpack('g' * num)
+			when 8 # Double 8-byte(s) wide
+				data.unpack('G' * num)
+			when 9 # BCD 0-byte(s) wide
+				"unsupported type 'BCD'(#{type})"
+			when 10 # Date 4-byte(s) wide
+				struct = {}
+				struct[:year], struct[:month], struct[:day] = data.unpack('s>CC' * num)
+				struct
+			when 11 # Time 4-byte(s) wide
+				struct = {}
+				struct[:hour], struct[:minute], struct[:second], struct[:hsecond] = data.unpack('CCCC' * num)
+				struct
+			when 12 # Thumb 10-byte(s) wide
+				struct = {}
+				struct[:d], struct[:u], struct[:c], struct[:n] = data.unpack('l>l>CC' * num)
+				struct
+			when 13 # Boolean 1-byte(s) wide
+				data.unpack('C' * num).map{|x| x == 0 ? false : true}
+			when 14 # Point 4-byte(s) wide
+				struct = {}
+				struct[:v], struct[:h] = data.unpack('s>s>' * num)
+				struct
+			when 15 # Rect 8-byte(s) wide
+				struct = {}
+				struct[:top], struct[:left], struct[:bottom], struct[:right] = data.unpack('s>s>s>s>' * num)
+				struct
+			when 16 # VPoint 8-byte(s) wide
+				struct = {}
+				struct[:v], struct[:h] = data.unpack('l>l>' * num)
+				struct
+			when 17 # VRect 16-byte(s) wide
+				struct = {}
+				struct[:top], struct[:left], struct[:bottom], struct[:right] = data.unpack('l>l>l>l>' * num)
+				struct
+			when 18 # PString 1-byte(s) wide
+				data[1..data[0].unpack("C").first]
+			when 19 # CString 1-byte(s) wide
+				data[0..-2]
+			when 20 # Tag 8-byte(s) wide
+				struct = {}
+				struct[:name], struct[:number] = data.unpack('l>l>' * num)
+				struct
+			when 21 # DeltaLZWcompression 1-byte(s) wide
+				# TODO: What is a "DeltaLZWcompression" compression? Implement it the right way.
+				"unsupported compression 'DeltaLZWcompression'(#{type})"
+			when 22 # LZWcompression 1-byte(s) wide
+				unlzw(data.unpack('C' * size * num))
+			when 23 # Directory 28-byte(s) wide
+				unpack_dir_entry(data)
+			when 24 # UserType 1-byte(s) wide
+				"user type 'UserType'(#{type}) => #{num} elements of #{size}-byte wide struct: " << data.unpack('C' * size * num).join(', ')
+			when 25 # CustomUserType 1-byte(s) wide
+				"user type 'CustomUserType'(#{type}) => #{num} elements of #{size}-byte wide struct: " << data.unpack('C' * size * num).join(', ')
+			when 26 # IString 1-byte(s) wide
+				# TODO: What is an "IString"? Implement it the right way.
+				data
+			when 27 # compressedByte 1-byte(s) wide
+				decrypt(data).unpack('C' * data_size)
+			when 28 # compressedShort 1-byte(s) wide
+				decrypt(data).unpack('C' * (data_size / 2))
+			when 29 # compressedIString 1-byte(s) wide
+				# TODO: What is an "IString"? Implement it the right way.
+				decrypt(data)
+			when 30 # compressedChar 1-byte(s) wide
+				decrypt(data).unpack('C' * data_size)
+			when 31 # compressedLong 1-byte(s) wide
+				decrypt(data).unpack('l>' * (data_size / 4))
+			when 32 # compressedDouble 1-byte(s) wide
+				decrypt(data).unpack('G' * (data_size / 8))
+			when 33 # compressedCString 1-byte(s) wide
+				decrypt(data)[0..-2]
+			when 34 # compressedPString 1-byte(s) wide
+				decrypted = decrypt(data)
+				decrypted[1..decrypted[0].unpack("C").first]
+			when 35 # compressedFloat 1-byte(s) wide
+				decrypt(data).unpack('g' * (data_size / 4))
+			when 128 # deltaComp
+				# TODO: What is a "deltaComp" compression? Implement it the right way.
+				"unsupported compression 'deltaComp' data type '#{type}'"
+			when 256 # LZWComp
+				unlzw(data.unpack('C' * size * num))
+			when 384 # deltaLZW
+				# TODO: What is a "deltaLZW" compression? Implement it the right way.
+				"unsupported compression 'deltaLZW'(#{type})"
+			when 1024 # user
+				"user type 'user'(#{type}) => #{num} elements of #{size}-byte wide struct: " << data.unpack('C' * size * num).join(', ')
+			else
+				"unsupported type '#{type}': " << data.unpack('C' * size * num).join(', ')
+			end
+		end
+
+		def inflate(compressed)
+			Zlib::Inflate.inflate compressed
+		end
+
+		def unlzw(compressed)
+		    dict_size = 256
+		    dictionary = Hash[ Array.new(dict_size) {|i| [i.chr, i.chr]} ]
+		 
+		    w = result = compressed.shift
+		    for k in compressed
+		        if dictionary.has_key?(k)
+		            entry = dictionary[k]
+		        elsif k == dict_size
+		            entry = w + w[0,1]
+		        else
+		            raise 'Bad compressed k: %s' % k
+		        end
+		        result += entry
+		 
+		        dictionary[dict_size] = w + entry[0,1]
+		        dict_size += 1
+		 
+		        w = entry
+		    end
+		    result
+		end			
+
+		def decrypt(encrypted)
+			@decipher.reset
+			@decipher.update(encrypted) + @decipher.final
+		end
+	end
+end

data/lib/ABIF/version.rb

@@ -0,0 +1,3 @@
+module ABIF
+  VERSION = "0.0.1"
+end

data/test/files/invalid.abif

@@ -0,0 +1,44 @@
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE
+NOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILENOTAVALIDABIFFILE

data/test/lib/ABIF/file_test.rb

@@ -0,0 +1,189 @@
+require_relative '../../test_helper'
+
+describe ABIF::File do
+	describe 'omitting file/filename' do
+		it 'raises an Error' do
+			Proc.new { ABIF::File.new }.must_raise ArgumentError
+		end
+	end
+	
+	describe 'invalid file/filehandle' do
+		it 'invalid file raises an Exception' do
+			Proc.new { ABIF::File.new('test/files/invalid.abif') }.must_raise IOError
+		end
+
+		it 'non-existing file raises an Exception' do
+			Proc.new { ABIF::File.new('test/files/foo.abif') }.must_raise IOError
+		end
+
+		it 'empty filehandle raises an Exception' do
+			Proc.new { ABIF::File.new(File.new) }.must_raise ArgumentError
+		end
+	end
+	
+	describe ABIF::File, 'valid filename' do
+		subject { ABIF::File.new('test/files/valid.abif') }
+
+		it 'is an instance of ABIF::File' do
+			subject.must_be_instance_of ABIF::File
+		end
+
+		it 'filetype is ABIF' do
+			subject.filetype.must_equal 'ABIF'
+		end
+
+		it 'fileversion is 101' do
+			subject.fileversion.must_equal 101
+		end
+
+		it 'data is a Hash' do
+			subject.data.must_be_kind_of Hash
+		end
+
+		{
+			'AEPt_1' => '329a2798ac4a2024f904a4900de7600d',
+			'AEPt_2' => '329a2798ac4a2024f904a4900de7600d',
+			'APFN_2' => '509a32e5f2979be945f61cddbd14622c',
+			'APXV_1' => '39c6844c921cf69656adaa2a8e4aea0c',
+			'APrN_1' => '509a32e5f2979be945f61cddbd14622c',
+			'APrV_1' => '3cf3aef9902754f1c9178e32f5fe1ddc',
+			'APrX_1' => '773e4cd95581ad061589066058e65d4f',
+			'ARTN_1' => '8d5162ca104fa7e79fe80fd92bb657fb',
+			'ASPF_1' => '35dba5d75538a9bbe0b4da4422759a0e',
+			'ASPt_1' => '220e850bfe79cb3526b375bc6dcdd2ef',
+			'ASPt_2' => '220e850bfe79cb3526b375bc6dcdd2ef',
+			'AUDT_1' => '49c8922d68864bb83c04879c1589a0fb',
+			'B1Pt_1' => 'af7e8bea94ff3c20159e249200b6aa18',
+			'B1Pt_2' => 'af7e8bea94ff3c20159e249200b6aa18',
+			'BCTS_1' => '162bb794a66800199501e1e9de7a15df',
+			'BufT_1' => '83a08dbe51340d001d2e7a3f8708e8cb',
+			'CCut_1' => 'b95b0b3bc23f39b3c04bc2baf211ba5b',
+			'CMNT_1' => '81bba32c7b86600386d96930ec17fda4',
+			'CTID_1' => '46f79adeafce95e4fdd7b6aebad1699e',
+			'CTNM_1' => '46f79adeafce95e4fdd7b6aebad1699e',
+			'CTOw_1' => 'c446a4c96a0fe001210b71144c2268f9',
+			'CTTL_1' => '74c70c8291e9dacf1935132d58229634',
+			'CpEP_1' => '35dba5d75538a9bbe0b4da4422759a0e',
+			'DATA_1' => 'c29a483afbeb83172305fb0803f3f264',
+			'DATA_2' => 'd9f5d923f13c66ff2385ee9cac1ba2f3',
+			'DATA_3' => 'e14a88b6353558b6af927de5ec1e070a',
+			'DATA_4' => '2b60b8f09786c6c182f53da105483bba',
+			'DATA_5' => '6f501928683d29942b95d5dad46e2e26',
+			'DATA_6' => 'f66e5d54b3606d9e060351c85a2ef733',
+			'DATA_7' => '7de240b0d5c835a9242555aaaa425d7a',
+			'DATA_8' => '272c59f929d32af7a1d655d175cf7a0e',
+			'DATA_9' => '66200730a3dc10020304032cc257dbd1',
+			'DATA_10' => '80238386cad29c86e1afc5d9a4d6622e',
+			'DATA_11' => '6d20453b6705c0144f954e9751b61c51',
+			'DATA_12' => '49061ea4bee661346a8d4ece6a606a3b',
+			'DCHT_1' => '8d5162ca104fa7e79fe80fd92bb657fb',
+			'DSam_1' => '35dba5d75538a9bbe0b4da4422759a0e',
+			'DySN_1' => 'c300e27b7c225652d4130f053f807199',
+			'Dye#_1' => 'e962e23c139e7252904b9221d9967442',
+			'DyeN_1' => 'b654f7796f95e5ed17096a82a0b28315',
+			'DyeN_2' => '207d360b49d1b72c0c35c89833757e5c',
+			'DyeN_3' => 'ac4b808acb1fc85fa0060bc92f489c69',
+			'DyeN_4' => '0ac0051af6ece5afeacf8e53e1dade59',
+			'DyeW_1' => 'f9639b0987d2ad3a3ae945ee29c889b4',
+			'DyeW_2' => '01df866ea9d6a730be6e319110ecfda0',
+			'DyeW_3' => 'c0280f103f34474ab0107746f80736fd',
+			'DyeW_4' => '47f2ba5a7a71c4646d8add9de01d8368',
+			'EPVt_1' => 'aea034f6800b624bf4d8d9fd4553d264',
+			'EVNT_1' => '10d4ece1db63d754b5ef1ba8fb635269',
+			'EVNT_2' => '9a81c64cb96fc6b7327bb2613c52e89d',
+			'EVNT_3' => 'fec688b3587dff8bb2c12a59cee0763e',
+			'EVNT_4' => '906341f47061764eb805b0b57b3cd7cc',
+			'FTab_1' => '21beecaab27020d9069dee9a570296d8',
+			'FVoc_1' => '139268d7ad20b68f72faa0b1691cac14',
+			'FWO__1' => '9f40a00e83bbaf678fe218b11f81d49e',
+			'Feat_1' => 'f9131fe168d95c26058ae03cff8e6be0',
+			'GTyp_1' => 'c7b375c0c538659369eee293b1cd8986',
+			'HCFG_1' => 'dbe992717239d8f63333a14fae4232c1',
+			'HCFG_2' => '9c0224cfb93aa409728cbac69fdf614b',
+			'HCFG_3' => '96cd52a8c96d12ba88c6ba36c316603d',
+			'HCFG_4' => 'fed17cd2cc23396408f8c2b480d71836',
+			'InSc_1' => '2a30f5f3b7d1a97cb6132480b992d984',
+			'InVt_1' => '423c57007341da0749aa1d8bb0da8042',
+			'LANE_1' => '6615ab6435d4f1da792f1e6fa230cb29',
+			'LIMS_1' => '6b3b0fa06550a54ba95f2e78dfb213b4',
+			'LNTD_1' => '8a8783242b7b77de148a06a0bab42ba9',
+			'LsrP_1' => '0a4f74e275e1168915d8d512ed22bf0c',
+			'MCHN_1' => 'ff90c90ed28916bb58eb2f56f425b41f',
+			'MODF_1' => '013f5a3ac5836a46be81dee59261f68d',
+			'MODL_1' => '59afde3cd75ce96556b9d5b3ce95fef5',
+			'NAVG_1' => '35dba5d75538a9bbe0b4da4422759a0e',
+			'NLNE_1' => '2375ef9e856b982a6f9e5b8fb903e6d7',
+			'NOIS_1' => '60afc12c44f69325eb1906a147339931',
+			'PBAS_1' => '214591fbf4e0c6032961ffb3dc685aaf',
+			'PBAS_2' => '214591fbf4e0c6032961ffb3dc685aaf',
+			'PCON_1' => '59cf9b876ec3410633cb72058af1cf8e',
+			'PCON_2' => '59cf9b876ec3410633cb72058af1cf8e',
+			'PDMF_1' => '94827116b0e6fec7abd084917c8cfc33',
+			'PDMF_2' => '94827116b0e6fec7abd084917c8cfc33',
+			'PLOC_1' => '87f2292a0f208ed70cb915c4d6c625e7',
+			'PLOC_2' => '87f2292a0f208ed70cb915c4d6c625e7',
+			'PSZE_1' => '2375ef9e856b982a6f9e5b8fb903e6d7',
+			'PTYP_1' => 'f75f3b63236ce233758cc898ebe835d0',
+			'PXLB_1' => 'f2577a6fc29b900fe7d4c6321346be48',
+			'RGNm_1' => '779dfa8b1b7a5cfd8063493b4bf2be46',
+			'RGOw_1' => 'b0b576a3a438583bd475a14acf06bf8b',
+			'RMXV_1' => '2f7bb230c70819aeb10b45a709bcf48f',
+			'RMdN_1' => '013f5a3ac5836a46be81dee59261f68d',
+			'RMdV_1' => '2f7bb230c70819aeb10b45a709bcf48f',
+			'RMdX_1' => '41b6d91073540a2a199bf9f089e11a29',
+			'RPrN_1' => '21d72202012057acf64ec7d3aa52ee42',
+			'RPrV_1' => '2f7bb230c70819aeb10b45a709bcf48f',
+			'RUND_1' => '21e7f6441ffe6ef6c36db98592ae0810',
+			'RUND_2' => '21e7f6441ffe6ef6c36db98592ae0810',
+			'RUND_3' => '21e7f6441ffe6ef6c36db98592ae0810',
+			'RUND_4' => '21e7f6441ffe6ef6c36db98592ae0810',
+			'RUNT_1' => '42a575cff8de9a296db610df9cff6f1f',
+			'RUNT_2' => '8647ea4a1090319b27562610d831172e',
+			'RUNT_3' => '1523ed7e16b541e809eb6acacf5f32c1',
+			'RUNT_4' => '337a52990fce3bea946d4fa60d0f51aa',
+			'Rate_1' => '9f1074af1ce98833fbf4775c5f3595cb',
+			'RunN_1' => '2048de7707e4fdc395175ce4784dce18',
+			'S/N%_1' => 'fbd3b15939b954654a38824ec1e82eb7',
+			'SCAN_1' => '329a2798ac4a2024f904a4900de7600d',
+			'SMED_1' => '0edefa708c51887ad9b3fbe1ea9e7e82',
+			'SMLt_1' => 'aed6e480b8aad696f3bb3a2781cd55d6',
+			'SMPL_1' => '172160c679614e93d5c07ef7b7a2441f',
+			'SPAC_1' => '3e58eb892f1ff04c1da6acf6509f976b',
+			'SPAC_2' => 'e991d1ef3f35a5da0b8b724490a6f21a',
+			'SPAC_3' => '3e58eb892f1ff04c1da6acf6509f976b',
+			'SVER_1' => 'a629005e3c810e8491172eebd622a57b',
+			'SVER_2' => 'cbd989d62be7257144760e24edeaf516',
+			'SVER_3' => '783e7db369d5e7d7d57e5c76a1dec609',
+			'Scal_1' => '8796ada1698c9940b7cf9264407731b1',
+			'Scan_1' => '329a2798ac4a2024f904a4900de7600d',
+			'TUBE_1' => 'aafe2f8af7d2109f20d5ae4c488bf1c6',
+			'Tmpr_1' => '1be08982f722684e69bdf6c5549d67ba',
+			'User_1' => 'c446a4c96a0fe001210b71144c2268f9',
+			'phAR_1' => '14a685bc2583777f837ed9d24798d915',
+			'phCH_1' => '89a93d4bcb2615549a98b93d2e2f5c96',
+			'phDY_1' => '7153f0402307a99a60929d7b5dcd886b',
+			'phQL_1' => 'e6cd5c7f942fc1c21557adbc97739b8c',
+			'phTR_1' => 'b95b0b3bc23f39b3c04bc2baf211ba5b',
+			'phTR_2' => '14a685bc2583777f837ed9d24798d915'
+		}.each do |key, md5|
+			it "MD5 of data['#{key}'] equals '#{md5}'" do
+				subject.data[key].wont_be_nil
+				Digest::MD5.hexdigest(subject.data[key].inspect).must_equal md5
+			end
+		end 
+	end
+
+	describe 'supported?' do
+		it 'return false on unsupported file' do
+			ABIF::File.supported?('test/files/invalid.abif').must_equal false
+		end
+
+		it 'return true on supported file' do
+			ABIF::File.supported?('test/files/valid.abif').must_equal true
+		end
+
+		it 'raise an exception on non-existing file' do
+			Proc.new { ABIF::File.supported?('test/files/foo.abif') }.must_raise IOError
+		end
+	end
+end

data/test/test_helper.rb

@@ -0,0 +1,4 @@
+gem 'minitest'
+require 'minitest/autorun'
+require 'minitest/pride'
+require File.expand_path('../../lib/ABIF.rb', __FILE__)

metadata

@@ -0,0 +1,121 @@
+--- !ruby/object:Gem::Specification
+name: ABIF
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Sascha Willuweit
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-10-04 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: thor
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  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: 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: ABIF file format reader/parse/plotter.
+email:
+- s@rprojekt.org
+executables:
+- abifcli
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- ABIF.gemspec
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/abifcli
+- lib/ABIF.rb
+- lib/ABIF/cli.rb
+- lib/ABIF/file.rb
+- lib/ABIF/version.rb
+- test/files/invalid.abif
+- test/files/valid.abif
+- test/lib/ABIF/file_test.rb
+- test/test_helper.rb
+homepage: https://github.com/545ch4/ABIF
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.0.6
+signing_key: 
+specification_version: 4
+summary: Handle/Parse/Plot ABIF (Applied Biosystems Genetic Analysis Data File Format)
+  FSA, AB1 and HID files.
+test_files:
+- test/files/invalid.abif
+- test/files/valid.abif
+- test/lib/ABIF/file_test.rb
+- test/test_helper.rb