2 $:.unshift File.join(File.dirname(__FILE__),'..','lib')
4 # Copyright (C) 2007-2010 Martin A. Hansen.
6 # This program is free software; you can redistribute it and/or
7 # modify it under the terms of the GNU General Public License
8 # as published by the Free Software Foundation; either version 2
9 # of the License, or (at your option) any later version.
11 # This program is distributed in the hope that it will be useful,
12 # but WITHOUT ANY WARRANTY; without even the implied warranty of
13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 # GNU General Public License for more details.
16 # You should have received a copy of the GNU General Public License
17 # along with this program; if not, write to the Free Software
18 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
20 # http://www.gnu.org/copyleft/gpl.html
22 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
24 # This software is part of the Biopieces framework (www.biopieces.org).
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
29 require 'maasha/fasta'
33 class FastaTest < Test::Unit::TestCase
34 def test_Fasta_get_entry_obtains_the_correct_seq_name
35 fasta = Fasta.new(StringIO.new(">test\nATCG\n"))
36 assert_equal("test", fasta.get_entry.seq_name)
39 def test_Fasta_get_entry_obtains_the_correct_seq_without_trailing_newlines
40 fasta = Fasta.new(StringIO.new(">test\nATCG"))
41 assert_equal("ATCG", fasta.get_entry.seq)
44 def test_Fasta_get_entry_obtains_the_correct_seq_with_trailing_newlines
45 fasta = Fasta.new(StringIO.new(">test\nATCG\n\n\n"))
46 assert_equal("ATCG", fasta.get_entry.seq)
49 def test_Fasta_get_entry_obtains_the_correct_type
50 fasta = Fasta.new(StringIO.new(">test\nATCG\n"), 'DNA')
51 assert_equal("dna", fasta.get_entry.type)
54 def test_Fasta_get_entry_rstrips_whitespace_from_seq_name
55 fasta = Fasta.new(StringIO.new(">test\n\r\t ATCG\n"))
56 assert_equal("test", fasta.get_entry.seq_name)
59 def test_Fasta_get_entry_strips_whitespace_from_seq
60 fasta = Fasta.new(StringIO.new(">test\n\r\t AT\n\r\t CG\n\r\t "))
61 assert_equal("ATCG", fasta.get_entry.seq)
64 def test_Fasta_get_entry_with_two_entries_obtain_correct
65 fasta = Fasta.new(StringIO.new(">test1\n\r\t AT\n\r\t CG\n\r\t \n>test2\n\r\t atcg\n"))
66 assert_equal("ATCG", fasta.get_entry.seq)
67 assert_equal("atcg", fasta.get_entry.seq)
70 def test_Fasta_get_entry_without_seq_name_raises
71 fasta = Fasta.new(StringIO.new("ATCG\n"))
72 assert_raise(FastaError) { fasta.get_entry }
75 def test_Fasta_get_entry_without_seq_raises
76 fasta = Fasta.new(StringIO.new(">test\n\n"))
77 assert_raise(FastaError) { fasta.get_entry }
80 def test_Fasta_get_entry_with_leading_newline_raises
81 fasta = Fasta.new(StringIO.new("\n>test\nATCG\n"))
82 assert_raise(FastaError) { fasta.get_entry }
86 # def test_Fasta_get_entry raises on missing > in seq_name
87 # fasta = Fasta.new(StringIO.new("test\nATCG\n"))
88 # assert_raise( FastaError ) { fasta.get_entry }