def test_from_index_and_length(self, glucagon_peptides, glucagon_seq):
# simple tests
index = self.protein_seq.index(self.pep_seq)
p = SequenceRange.from_index(index, length=len(self.pep_seq))
self._assert(p, self.pep_seq, self.protein_seq)
# all peptides
for (start, stop, seq) in glucagon_peptides:
p = SequenceRange.from_index(glucagon_seq.index(seq),
length=len(seq))
self._assert(p, seq, glucagon_seq)
with pytest.raises(ValueError):
SequenceRange.from_index(SequenceRange(10), length=20)
def get_clusters(cls, h_cluster):
clusters = {}
for n_clust in range(1, h_cluster.max() + 1):
cluster_indexes = np.where(h_cluster == n_clust)[0]
clusters[n_clust] = SequenceRange.from_index(
cluster_indexes[0], cluster_indexes[-1])
return clusters
def test___repr__(self):
assert repr(SequenceRange(10, 20)) == "SequenceRange(10, 20, seq=None)"
seq = "A" * 11
assert repr(SequenceRange(10, 20, seq=seq)) == \
'SequenceRange(10, 20, seq="{}")'.format(seq)
assert repr(SequenceRange(10, 20).pos) == "(10, 20)"
assert repr(SequenceRange.from_index(10, 20).index) == "(10, 20)"
def test_from_index(self, glucagon_peptides, glucagon_seq):
pep_start_index = 5
pep_stop_index = 8
p_index = SequenceRange.from_index(pep_start_index, pep_stop_index)
p_index2 = SequenceRange.from_index((pep_start_index, pep_stop_index))
assert p_index == p_index2
p = SequenceRange(self.pep_start, self.pep_stop)
assert p == p_index
assert self.pep_seq[0] == self.protein_seq[p_index.start.index]
assert self.pep_seq[-1] == self.protein_seq[p_index.stop.index]
with pytest.raises(ValueError):
SequenceRange.from_index(SequenceRange(10), 10)
with pytest.raises(ValueError):
SequenceRange.from_index(10, SequenceRange(10))
with pytest.raises(ValueError):
SequenceRange.from_index(SequenceRange(10), SequenceRange(10))
