--- /dev/null
+# 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 the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program 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 this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'seq'
+require 'zlib'
+
+# Error class for all exceptions to do with FASTQ.
+class FastqError < StandardError; end
+
+class Fastq
+ include Enumerable
+
+ # Class method allowing open to be used on (zipped) files.
+ # See File.open.
+ def self.open(*args)
+ ios = self.zopen(*args)
+
+ if block_given?
+ begin
+ yield ios
+ ensure
+ ios.close
+ end
+ else
+ return ios
+ end
+ end
+
+ def initialize(io, type=nil)
+ @io = io
+ @type = type
+ end
+
+ # Method to close ios.
+ def close
+ @io.close
+ end
+
+ # Iterator method for parsing FASTQ enries.
+ def each
+ while entry = get_entry do
+ yield entry
+ end
+ end
+
+ # Method to get the next FASTQ entry form an ios and return this
+ # as a Seq object. If no entry is found or eof then nil is returned.
+ def get_entry
+ begin
+ seq_name = @io.gets.chomp!
+ seq = @io.gets.chomp!
+ qual_name = @io.gets.chomp!
+ qual = @io.gets.chomp!
+
+ entry = Seq.new
+ entry.type = @type.nil? ? nil : @type.downcase
+ entry.seq = seq
+ entry.seq_name = seq_name[1 .. seq_name.length]
+ entry.qual = qual
+
+ entry
+ rescue
+ nil
+ end
+ end
+
+ # TODO - this should be some custom to_s method instead.
+ def puts(record)
+ if record.has_key? :SEQ_NAME and record.has_key? :SEQ
+ @io.print ">#{record[:SEQ_NAME]}\n"
+ @io.print "#{record[:SEQ]}\n"
+ end
+ end
+
+ private
+
+ # Helper method to return an ios to a file that may be zipped in which case
+ # the ios is unzipped on the fly. See File.open.
+ def self.zopen(*args)
+ ios = File.open(*args)
+
+ begin
+ ios = Zlib::GzipReader.new(ios)
+ rescue
+ ios.rewind
+ end
+
+ self.new(ios)
+ end
+end
+
+
+__END__
--- /dev/null
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# 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 the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program 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 this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'test/unit'
+require 'align'
+require 'pp'
+
+class MatrixTest < Test::Unit::TestCase
+ def test_Matrix_initialize_raise_on_bad_rows_value
+ [-2, 0].each do |val|
+ assert_raise(Align::MatrixError) { Align::Matrix.new(val, 2) }
+ end
+ end
+
+ def test_Matrix_initialize_raise_on_bad_cols_value
+ [-2, 0].each do |val|
+ assert_raise(Align::MatrixError) { Align::Matrix.new(2, val) }
+ end
+ end
+
+ def test_Matrix_initialize_dont_raise_on_ok_values
+ assert_nothing_raised { Align::Matrix.new(2, 2) }
+ end
+
+ def test_Matrix_set_raise_on_bad_row_value
+ matrix = Align::Matrix.new(2,3)
+ [-1, 2, 3].each do |row|
+ assert_raise(Align::MatrixError) { matrix.set(row, 2) }
+ end
+ end
+
+ def test_Matrix_set_raise_on_bad_col_value
+ matrix = Align::Matrix.new(2,3)
+ [-1, 3, 4].each do |col|
+ assert_raise(Align::MatrixError) { matrix.set(1, col) }
+ end
+ end
+
+ def test_Matrix_set_dont_raise_on_ok_values
+ matrix = Align::Matrix.new(2,3)
+ (0 ... 2).each do |row|
+ (0 ... 3).each do |col|
+ matrix.set(row, col)
+ end
+ end
+ end
+
+ def test_Matrix_set_returns_corretly
+ matrix = Align::Matrix.new(2,3)
+ assert_equal([0, 0, 1, 0, 0, 0], matrix.set(0, 2))
+ end
+
+ def test_Matrix_to_s_returns_correctly
+ matrix = Align::Matrix.new(2,3)
+ matrix.set(0,0)
+ matrix.set(0,2)
+ matrix.set(1,0)
+ matrix.set(1,2)
+ assert_equal("1 0 1\n1 0 1\n", matrix.to_s)
+ end
+
+ def test_Matrix_slice_raise_on_bad_row_beg_values
+ matrix = Align::Matrix.new(4,4)
+ [-1, 4].each do |val|
+ assert_raise(Align::MatrixError) { matrix.slice(val, 1, 1, 1) }
+ end
+ end
+
+ def test_Matrix_slice_raise_on_bad_row_end_values
+ matrix = Align::Matrix.new(4,4)
+ [-1, 2, 4].each do |val|
+ assert_raise(Align::MatrixError) { matrix.slice(3, val, 1, 1) }
+ end
+ end
+
+ def test_Matrix_slice_raise_on_bad_col_beg_values
+ matrix = Align::Matrix.new(4,4)
+ [-1, 4].each do |val|
+ assert_raise(Align::MatrixError) { matrix.slice(1, 1, val, 1) }
+ end
+ end
+
+ def test_Matrix_slice_raise_on_bad_col_end_values
+ matrix = Align::Matrix.new(4,4)
+ [-1, 2, 4].each do |val|
+ assert_raise(Align::MatrixError) { matrix.slice(1, 1, 3, val) }
+ end
+ end
+
+ def test_Matrix_slice_dont_raise_on_ok_values
+ matrix = Align::Matrix.new(4,4)
+ (0 ... 4).each do |val|
+ assert_nothing_raised {matrix.slice(val, val, val, val) }
+ end
+ end
+
+ def test_Matrix_slice_returns_correctly
+ matrix = Align::Matrix.new(4,4)
+ matrix.set(1,1)
+ matrix.set(2,2)
+ assert_equal( "0 0\n0 1\n", matrix.slice(0, 1, 0, 1).to_s )
+ assert_equal( "1 0\n0 1\n", matrix.slice(1, 2, 1, 2).to_s )
+ assert_equal( "1 0\n0 0\n", matrix.slice(2, 3, 2, 3).to_s )
+ end
+end
+
--- /dev/null
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# 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 the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program 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 this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'test/unit'
+require 'fastq'
+require 'stringio'
+require 'pp'
+
+class FastqTest < Test::Unit::TestCase
+ def setup
+ @io = StringIO.new("@test1\nATCG\n+\nABCD\n@test2\natcg\n+test2\n@ABG\n")
+ @fastq = Fastq.new(@io)
+ end
+
+ def test_Fastq_get_entry_obtains_the_correct_seq_name
+ assert_equal("test1", @fastq.get_entry.seq_name)
+ end
+
+ def test_Fasta_get_entry_obtains_the_correct_type
+ fastq = Fastq.new(@io, 'DNA')
+ assert_equal("dna", fastq.get_entry.type)
+ end
+
+ def test_Fastq_get_entry_with_two_entries_obtain_correct
+ assert_equal("ATCG", @fastq.get_entry.seq)
+ assert_equal("atcg", @fastq.get_entry.seq)
+ end
+
+ def test_Fastq_each_loop_ends_correctly
+ @fastq.each do |entry|
+ end
+ end
+end
projects / biopieces.git / commitdiff