#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
require 'maasha/seq'
require 'test/unit'
+require 'test/helper'
require 'pp'
class TestTrim < Test::Unit::TestCase
@entry = Seq.new
end
- def test_Trim_quality_trim_with_missing_seq_raises
+ test "Seq.quality_trim with missing seq raises" do
@entry.qual = "hhhh"
assert_raise(TrimError) { @entry.quality_trim_right(20) }
assert_raise(TrimError) { @entry.quality_trim_right!(20) }
assert_raise(TrimError) { @entry.quality_trim!(20) }
end
- def test_Trim_quality_trim_with_missing_qual_raises
+ test "Seq.quality_trim with missing qual raises" do
@entry.seq = "ATCG"
assert_raise(TrimError) { @entry.quality_trim_right(20) }
assert_raise(TrimError) { @entry.quality_trim_right!(20) }
assert_raise(TrimError) { @entry.quality_trim!(20) }
end
- def test_Trim_quality_trim_with_bad_min_raises
+ test "Seq.quality_trim with bad min raises" do
@entry.seq = "ATCG"
@entry.qual = "hhhh"
end
end
- def test_Trim_quality_trim_with_ok_min_dont_raise
+ test "Seq.quality_trim with ok min dont raise" do
@entry.seq = "ATCG"
@entry.qual = "hhhh"
end
end
- def test_Trim_quality_trim_right_returns_correctly
+ test "Seq.quality_trim_right returns correctly" do
@entry.seq = "AAAAATCG"
- @entry.qual = "hhhhhgfe"
+ @entry.qual = "IIIIIHGF"
new_entry = @entry.quality_trim_right(38)
assert_equal("AAAAATC", new_entry.seq)
- assert_equal("hhhhhgf", new_entry.qual)
+ assert_equal("IIIIIHG", new_entry.qual)
assert_equal("AAAAATCG", @entry.seq)
- assert_equal("hhhhhgfe", @entry.qual)
+ assert_equal("IIIIIHGF", @entry.qual)
end
- def test_Trim_quality_trim_right_bang_returns_correctly
+ test "Seq.quality_trim_right! returns correctly" do
@entry.seq = "AAAAATCG"
- @entry.qual = "hhhhhgfe"
+ @entry.qual = "IIIIIHGF"
@entry.quality_trim_right!(38)
assert_equal("AAAAATC", @entry.seq)
- assert_equal("hhhhhgf", @entry.qual)
+ assert_equal("IIIIIHG", @entry.qual)
end
- def test_Trim_quality_trim_right_with_all_low_qual_returns_correctly
+ test "Seq.quality_trim_right! with all low qual returns correctly" do
@entry.seq = "GCTAAAAA"
@entry.qual = "@@@@@@@@"
@entry.quality_trim_right!(38)
assert_equal("", @entry.qual)
end
- def test_Trim_quality_trim_left_returns_correctly
+ test "Seq.quality_trim_left returns correctly" do
@entry.seq = "GCTAAAAA"
- @entry.qual = "efghhhhh"
+ @entry.qual = "FGHIIIII"
new_entry = @entry.quality_trim_left(38)
assert_equal("CTAAAAA", new_entry.seq)
- assert_equal("fghhhhh", new_entry.qual)
+ assert_equal("GHIIIII", new_entry.qual)
assert_equal("GCTAAAAA", @entry.seq)
- assert_equal("efghhhhh", @entry.qual)
+ assert_equal("FGHIIIII", @entry.qual)
end
- def test_Trim_quality_trim_left_bang_returns_correctly
+ test "Seq.quality_trim_left! returns correctly" do
@entry.seq = "GCTAAAAA"
- @entry.qual = "efghhhhh"
+ @entry.qual = "FGHIIIII"
@entry.quality_trim_left!(38)
assert_equal("CTAAAAA", @entry.seq)
- assert_equal("fghhhhh", @entry.qual)
+ assert_equal("GHIIIII", @entry.qual)
end
- def test_Trim_quality_trim_left_with_all_low_qual_returns_correctly
+ test "Seq.quality_trim_left! with all low qual returns correctly" do
@entry.seq = "GCTAAAAA"
@entry.qual = "@@@@@@@@"
@entry.quality_trim_left!(38)
assert_equal("", @entry.qual)
end
- def test_Trim_quality_trim_returns_correctly
+ test "Seq.quality_trim returns correctly" do
@entry.seq = "GCTAAAAAGTG"
- @entry.qual = "efghhhhhgfe"
+ @entry.qual = "FGHIIIIIHGF"
new_entry = @entry.quality_trim(38)
assert_equal("CTAAAAAGT", new_entry.seq)
- assert_equal("fghhhhhgf", new_entry.qual)
+ assert_equal("GHIIIIIHG", new_entry.qual)
assert_equal("GCTAAAAAGTG", @entry.seq)
- assert_equal("efghhhhhgfe", @entry.qual)
+ assert_equal("FGHIIIIIHGF", @entry.qual)
end
- def test_Trim_quality_trim_bang_returns_correctly
+ test "Seq.quality_trim! returns correctly" do
@entry.seq = "GCTAAAAAGTG"
- @entry.qual = "efghhhhhgfe"
+ @entry.qual = "FGHIIIIIHGF"
@entry.quality_trim!(38)
assert_equal("CTAAAAAGT", @entry.seq)
- assert_equal("fghhhhhgf", @entry.qual)
+ assert_equal("GHIIIIIHG", @entry.qual)
end
- def test_Trim_quality_trim_with_min_len_bang_returns_correctly
+ test "Seq.quality_trim! with min len bang returns correctly" do
@entry.seq = "GCTCAAACGTG"
- @entry.qual = "hdefghgfedh"
+ @entry.qual = "IEFGHIHGFEI"
@entry.quality_trim!(37, 2)
assert_equal("TCAAACG", @entry.seq)
- assert_equal("efghgfe", @entry.qual)
+ assert_equal("FGHIHGF", @entry.qual)
end
- def test_Trim_quality_trim_with_all_low_qual_returns_correctly
+ test "Seq.quality_trim! with all low qual returns correctly" do
@entry.seq = "GCTCAAACGTG"
@entry.qual = "@@@@@@@@@@@"
@entry.quality_trim!(37, 2)