def test_write_fasta():
A = Alphabet('ACGT')
S = A.parse('AAA', name='foo')
T = A.parse('TTT', name='bar')
with NamedTemporaryFile() as f:
write_fasta(f, [S, T])
f.seek(0)
assert [s for s, _ in read_fasta(f, A)] == [S, T], \
'read_fasta(write_fasta()) should be identity'
f = StringIO('')
write_fasta(f, [S, T])
f.seek(0)
assert f.read() == '>foo\nAAA\n>bar\nTTT\n', 'should work on StringIO'
f = StringIO('')
# duplicate names not allowed
with pytest.raises(AssertionError):
write_fasta(f, [S, S])
f = StringIO('')
S = A.parse('AAATTT', name='foo')
write_fasta(f, [S], width=3) # should take 3 lines
f.seek(0)
assert sum(1 for _ in f) == 3, 'FASTA width should be modifiable'
def test_read_fasta_basic():
A = Alphabet('ACGT')
with NamedTemporaryFile() as f:
f.write('> name1\nAAA\n\nTTT')
f.flush()
f.seek(0)
recs = [r for r in read_fasta(f, A)]
assert len(recs) == 1, 'should work when reading from file'
assert recs[0][0] == A.parse('AAATTT', name='name1'), \
'should properly parse what is in the file'
assert isinstance(recs[0][0], NamedSequence), \
'should return NamedSequence objects'
assert recs[0][1] == 0, 'should report the right file positions'
# duplicate names not allowed
with pytest.raises(AssertionError):
[r for r in read_fasta(StringIO('>name\nAAA\n> name\nTTT\n'), A)]
def test_read_fasta_advanced():
A = Alphabet('ACGT')
fasta = '>name0\nAAA\n\n>name1\nTTT\n\n>name2\nCCC\n>name3\nGGG'
f = StringIO(fasta)
recs = [r for r in read_fasta(f, A)]
assert len(recs) == fasta.count('>'), 'should work with StringIO'
# check loading from position
for idx in range(4):
assert recs[idx][1] == fasta.index('>name%d' % idx), \
'should report the right file positions'
f.seek(recs[idx][1])
assert next(read_fasta(f, A, num=1))[0] == recs[idx][0], \
'should be able to read single sequences from known positions'
f.seek(recs[1][1])
assert [r for r in read_fasta(f, A, num=2)] == recs[1:3], \
'should be able to read known number of sequences from known positions'