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Rework get_examples_* #112

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Jun 18, 2024
Merged

Rework get_examples_* #112

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52 changes: 32 additions & 20 deletions tests/lsbase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,45 +67,57 @@ def get_examples_haploid(self, ts, include_ancestors):
ref_panel = self.get_ancestral_haplotypes(ts)
else:
ref_panel = ts.genotype_matrix()
num_sites = ref_panel.shape[0]
# Take some haplotypes as queries from the reference panel.
query1 = ref_panel[:, 0].reshape(1, num_sites)
query2 = ref_panel[:, 1].reshape(1, num_sites)
num_sites = ref_panel.shape[0]
query_1 = ref_panel[:, 0].reshape(1, num_sites)
query_1 = np.append(query_1[:2], query_1[2:]).reshape(1, num_sites)
query_2 = query_1[::-1]
# Create queries with MISSING.
query_miss_last = query1.copy()
query_miss_last = query_1.copy()
query_miss_last[0, -1] = core.MISSING
query_miss_mid = query1.copy()
query_miss_mid = query_1.copy()
query_miss_mid[0, ts.num_sites // 2] = core.MISSING
query_miss_most = query1.copy()
query_miss_most[0, 2:] = core.MISSING
queries = [query1, query2, query_miss_last, query_miss_mid, query_miss_most]
# Exclude the arbitrarily chosen queries from the reference panel.
ref_panel = ref_panel[:, 2:]
query_miss_most_1 = query_1.copy()
query_miss_most_1[0, 2:] = core.MISSING
query_miss_most_2 = query_miss_most_1[::-1]
queries = [
query_1,
query_2,
query_miss_last,
query_miss_mid,
query_miss_most_1,
query_miss_most_2,
]
return ref_panel, queries

def get_examples_diploid(self, ts, include_ancestors):
if include_ancestors:
ref_panel = self.get_ancestral_haplotypes(ts)
else:
ref_panel = ts.genotype_matrix()
num_sites = ref_panel.shape[0]
# Take some haplotypes as queries from the reference panel.
query_1 = np.zeros((2, num_sites), dtype=np.int32) - np.inf
num_sites = ref_panel.shape[0]
query_1 = np.zeros((2, num_sites), dtype=np.int8) - np.inf
query_1[0, :] = ref_panel[:, 0].reshape(1, num_sites)
query_1[1, :] = ref_panel[:, 1].reshape(1, num_sites)
query_2 = np.zeros((2, num_sites), dtype=np.int32) - np.inf
query_2[0, :] = ref_panel[:, 2].reshape(1, num_sites)
query_2[1, :] = ref_panel[:, 3].reshape(1, num_sites)
query_1 = np.append(query_1[:, :2], query_1[:, 2:]).reshape(2, num_sites)
query_2 = query_1[:, ::-1]
# Create queries with MISSING.
query_miss_last = query_1.copy()
query_miss_last[:, -1] = core.MISSING
query_miss_mid = query_1.copy()
query_miss_mid[:, ts.num_sites // 2] = core.MISSING
query_miss_most = query_1.copy()
query_miss_most[:, 1:] = core.MISSING
queries = [query_1, query_2, query_miss_last, query_miss_mid, query_miss_most]
# Exclude the arbitrarily chosen queries from the reference panel.
# ref_panel = ref_panel[:, 4:]
query_miss_most_1 = query_1.copy()
query_miss_most_1[:, 2:] = core.MISSING
query_miss_most_2 = query_miss_most_1[:, ::-1]
queries = [
query_1,
query_2,
query_miss_last,
query_miss_mid,
query_miss_most_1,
query_miss_most_2,
]
return ref_panel, queries

def get_examples_pars(
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