def reverse
self.seq.reverse!
self.qual.reverse! if self.qual
def reverse
self.seq.reverse!
self.qual.reverse! if self.qual
end
# Method that complements sequence including ambiguity codes.
end
# Method that complements sequence including ambiguity codes.
self.subseq(start, length)
end
self.subseq(start, length)
end
+ def quality_trim(min)
+ end
+
+ def quality_trim_right(min)
+ end
+
+ def quality_trim_left(min)
+ end
+
+ def quality_trim!(min)
+ end
+
+ def quality_trim_right!(min)
+ end
+
+ def quality_trim_left!(min)
+ end
+
# Method that returns the residue compositions of a sequence in
# a hash where the key is the residue and the value is the residue
# count.
# Method that returns the residue compositions of a sequence in
# a hash where the key is the residue and the value is the residue
# count.
def test_Seq_reverse_returns_correctly
@entry.seq = "ATCG"
def test_Seq_reverse_returns_correctly
@entry.seq = "ATCG"
- assert_equal("GCTA", @entry.reverse)
+ assert_equal("GCTA", @entry.reverse.seq)
end
def test_Seq_complement_raises_if_no_sequence
end
def test_Seq_complement_raises_if_no_sequence
def test_Seq_reverse_complement_for_DNA_is_correct
@entry.seq = 'ATCGatcg'
@entry.type = 'dna'
def test_Seq_reverse_complement_for_DNA_is_correct
@entry.seq = 'ATCGatcg'
@entry.type = 'dna'
- assert_equal("cgatCGAT", @entry.reverse_complement)
+ assert_equal("cgatCGAT", @entry.reverse_complement.seq)
end
def test_Seq_reverse_complement_for_RNA_is_correct
@entry.seq = 'AUCGaucg'
@entry.type = 'rna'
end
def test_Seq_reverse_complement_for_RNA_is_correct
@entry.seq = 'AUCGaucg'
@entry.type = 'rna'
- assert_equal("cgauCGAU", @entry.reverse_complement)
+ assert_equal("cgauCGAU", @entry.reverse_complement.seq)
end
def test_Seq_hamming_distance_returns_correctly
end
def test_Seq_hamming_distance_returns_correctly