2 $:.unshift File.join(File.dirname(__FILE__), '..', '..')
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 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
30 require 'maasha/fasta'
33 class FastaTest < Test::Unit::TestCase
34 test "#get_entry obtains the correct seq_name" do
35 fasta = Fasta.new(StringIO.new(">test\nATCG\n"))
36 assert_equal("test", fasta.get_entry.seq_name)
39 test "#get_entry obtains the correct seq without trailing newlines" do
40 fasta = Fasta.new(StringIO.new(">test\nATCG"))
41 assert_equal("ATCG", fasta.get_entry.seq)
44 test "#get_entry obtains the correct seq with trailing newlines" do
45 fasta = Fasta.new(StringIO.new(">test\nATCG\n\n\n"))
46 assert_equal("ATCG", fasta.get_entry.seq)
49 test "#get_entry rstrips whitespace from seq_name" do
50 fasta = Fasta.new(StringIO.new(">test\n\r\t ATCG\n"))
51 assert_equal("test", fasta.get_entry.seq_name)
54 test "#get_entry strips whitespace from seq" do
55 fasta = Fasta.new(StringIO.new(">test\n\r\t AT\n\r\t CG\n\r\t "))
56 assert_equal("ATCG", fasta.get_entry.seq)
59 test "#get_entry with two entries obtain correct" do
60 fasta = Fasta.new(StringIO.new(">test1\n\r\t AT\n\r\t CG\n\r\t \n>test2\n\r\t atcg\n"))
61 assert_equal("ATCG", fasta.get_entry.seq)
62 assert_equal("atcg", fasta.get_entry.seq)
65 test "#get_entry without seq_name raises" do
66 fasta = Fasta.new(StringIO.new("ATCG\n"))
67 assert_raise(FastaError) { fasta.get_entry }
70 test "#get_entry without seq raises" do
71 fasta = Fasta.new(StringIO.new(">test\n\n"))
72 assert_raise(FastaError) { fasta.get_entry }
75 test "#get_entry with leading newline raises" do
76 fasta = Fasta.new(StringIO.new("\n>test\nATCG\n"))
77 assert_raise(FastaError) { fasta.get_entry }
81 # test "#get_entry raises on missing > in seq_name" do
82 # fasta = Fasta.new(StringIO.new("test\nATCG\n"))
83 # assert_raise( FastaError ) { fasta.get_entry }