def test_constructor(self):
"""Test Sequence construction.
"""
_ = sequence.Sequence(name='test', seq='aaa')
_ = sequence.Sequence(name='test')
_ = sequence.Sequence(seq='aaa')
_ = sequence.Sequence()
def test_get_fasta(self):
"""Test the get_fasta method.
"""
name = 'test_name'
seq_str = 'abcdefg'
seq = sequence.Sequence(name=name, seq=seq_str)
assert seq.get_fasta() == '>{}\n{}'.format(name, seq_str)
def test_set_cont_values(self):
"""Test the set_cont_values method.
"""
seq = sequence.Sequence(name='test')
new_vals = [1, 2, 3, 4, 5]
seq.set_cont_values(new_vals)
assert seq.cont_values == new_vals
def test_get_fastq(self):
"""Test the get_fastq method."""
name = 'test_name'
seq_str = 'abcdefg'
qual_str = 'abcdefg'
seq = sequence.Sequence(name=name, seq=seq_str)
seq.set_qualstr(qual_str)
assert seq.get_fastq() == '@{}\n{}\n+\n{}'.format(
name, seq_str, qual_str)
def test_set_qualarr(self):
"""Test the set_qualarr function.
Note:
* Only modifies qualstr if it was an empty string.
"""
qual = [1, 2, 3, 4, 5]
seq2_qualstr = 'abcdefg'
seq1 = sequence.Sequence()
seq2 = sequence.Sequence()
seq2.set_qualstr(seq2_qualstr)
# Set qualarr for sequences
seq1.set_qualarr(qual)
seq2.set_qualarr(qual)
# qualarr should be the same for both
assert seq1.qualarr == seq2.qualarr
# qualstr should be different as seq2 should not have changed
assert seq1.qualstr != seq2.qualstr
assert seq2.qualstr == seq2_qualstr
def test_set_qualstr(self):
"""Test the set_qualstr method.
Note:
* Only modifies qualarr if it is an empty list.
"""
qual = 'abcdefg'
seq1 = sequence.Sequence()
seq2 = sequence.Sequence()
seq2_qualarr = [1, 2, 3, 4, 5]
seq2.set_qualarr(seq2_qualarr)
# Set qualstr for sequences
seq1.set_qualstr(qual)
seq2.set_qualstr(qual)
# qualstr should be the same for both
assert seq1.qualstr == seq2.qualstr
# qualarr should be different as seq2 should not have changed
assert seq1.qualarr != seq2.qualarr
assert seq2.qualarr == seq2_qualarr