entry_overlap = @entry1[-1 * overlap .. -1]
end
entry_overlap = @entry1[-1 * overlap .. -1]
end
+ entry_left.seq.upcase!
+ entry_right.seq.upcase!
entry_merged = entry_left + entry_overlap + entry_right
entry_merged.seq_name = @entry1.seq_name + ":overlap=#{overlap}:hamming=#{hamming_dist}"
entry_merged = entry_left + entry_overlap + entry_right
entry_merged.seq_name = @entry1.seq_name + ":overlap=#{overlap}:hamming=#{hamming_dist}"
end
test "Assemble.pair with overlap returns the correctly" do
end
test "Assemble.pair with overlap returns the correctly" do
- assert_equal("atcgatc", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "gatc")).seq)
- assert_equal("atcgat", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "cgat")).seq)
- assert_equal("atcga", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "tcga")).seq)
+ assert_equal("ATCgATC", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "gatc")).seq)
+ assert_equal("ATcgAT", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "cgat")).seq)
+ assert_equal("AtcgA", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "tcga")).seq)
assert_equal("atcg", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "atcg")).seq)
end
test "Assemble.pair with overlap and overlap_min returns correctly" do
assert_nil(Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "gatc"), :overlap_min => 2))
assert_equal("atcg", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "atcg")).seq)
end
test "Assemble.pair with overlap and overlap_min returns correctly" do
assert_nil(Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "gatc"), :overlap_min => 2))
- assert_equal("atcgat", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "cgat"), :overlap_min => 2).seq)
+ assert_equal("ATcgAT", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "cgat"), :overlap_min => 2).seq)
end
test "Assemble.pair with overlap and overlap_max returns correctly" do
end
test "Assemble.pair with overlap and overlap_max returns correctly" do
- assert_equal("atcga", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "tcga"), :overlap_max => 3).seq)
+ assert_equal("AtcgA", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "tcga"), :overlap_max => 3).seq)
assert_nil(Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "atcg"), :overlap_max => 3))
end
assert_nil(Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "atcg"), :overlap_max => 3))
end