Reorganise

python/tests/beagle.py

@@ -45,6 +45,8 @@
 
 import numpy as np
 
+import _tskit
+
 
 def convert_to_genetic_map_position(pos):
     """
@@ -642,3 +644,49 @@ def run_beagle(ref_h, query_h, pos, miscall_rate=0.0001, ne=1e6, debug=False):
         print(imputed_alleles)
     assert len(imputed_alleles) == x
     return (imputed_alleles, i_allele_probs)
+
+
+def run_tsimpute(ref_ts, query_h, pos, mu, rho):
+    """
+    Run the simplified BEAGLE algorithm above on a tree sequence.
+
+    :param numpy.ndarray ref_h: Reference haplotypes.
+    :param numpy.ndarray query_h: One query haplotype.
+    :param numpy.ndarray pos: Site positions of all the markers.
+    :param numpy.ndarray mu: Mismatch probabilities.
+    :param numpy.ndarray rho: Switch probabilities.
+    :param bool debug: Whether to print intermediate results.
+    :return: Imputed alleles and interpolated allele probabilities.
+    :rtype: list(numpy.ndarray, numpy.ndarray)
+    """
+    # Prepare marker positions.
+    genotyped_site_ids = np.where(query_h != -1)[0]
+    genotyped_pos = pos[genotyped_site_ids]
+    imputed_site_ids = np.where(query_h == -1)[0]
+    imputed_pos = pos[imputed_site_ids]
+    # Prepare reference haplotypes.
+    ref_ts_m = ref_ts.delete_sites(site_ids=imputed_site_ids)
+    ref_h_m = ref_ts_m.genotype_matrix()
+    ref_ts_x = ref_ts.delete_sites(site_ids=genotyped_site_ids)
+    ref_h_x = ref_ts_x.genotype_matrix()
+    query_h_m = query_h[genotyped_site_ids]
+    # Get forward and backward matrices from ts.
+    fm = _tskit.CompressedMatrix(ref_ts_m._ll_tree_sequence)
+    bm = _tskit.CompressedMatrix(ref_ts_m._ll_tree_sequence)
+    ls_hmm = _tskit.LsHmm(ref_ts_m._ll_tree_sequence, mu, rho, acgt_alleles=True)
+    ls_hmm.forward_matrix(query_h_m.T, fm)
+    ls_hmm.backward_matrix(query_h_m.T, fm.normalisation_factor, bm)
+    # Compute state probability matrix.
+    sm = compute_state_probability_matrix(
+        fm.decode(),
+        bm.decode(),
+        ref_h_m,
+        query_h_m,
+    )
+    # Interpolate allele probabilities.
+    i_allele_probs = interpolate_allele_probabilities(
+        sm, ref_h_x, genotyped_pos, imputed_pos
+    )
+    # Get MAP alleles at imputed markers.
+    imputed_alleles = get_map_alleles(i_allele_probs)
+    return (imputed_alleles, i_allele_probs)

python/tests/test_imputation.py

@@ -6,11 +6,7 @@
 import numpy as np
 import pytest
 
-import _tskit
 import tskit
-from tests.beagle import compute_state_probability_matrix
-from tests.beagle import get_map_alleles
-from tests.beagle import interpolate_allele_probabilities
 from tests.beagle import run_beagle
 
 
@@ -630,35 +626,3 @@ def parse_matrix(csv_text):
     # This returns a record array, which is essentially the same as a
     # pandas dataframe, which we can access via df["m"] etc.
     return np.lib.npyio.recfromcsv(io.StringIO(csv_text))
-
-
-def run_tsimpute(ref_ts, query_h, pos, mu, rho):
-    # Prepare marker positions.
-    genotyped_site_ids = np.where(query_h != -1)[0]
-    genotyped_pos = pos[genotyped_site_ids]
-    imputed_site_ids = np.where(query_h == -1)[0]
-    imputed_pos = pos[imputed_site_ids]
-    # Prepare reference haplotypes.
-    ref_ts_m = ref_ts.delete_sites(site_ids=imputed_site_ids)
-    ref_h_m = ref_ts_m.genotype_matrix()
-    ref_ts_x = ref_ts.delete_sites(site_ids=genotyped_site_ids)
-    ref_h_x = ref_ts_x.genotype_matrix()
-    query_h_m = query_h[genotyped_site_ids]
-    # Get forward and backward matrices from ts.
-    fm = _tskit.CompressedMatrix(ref_ts_m._ll_tree_sequence)
-    bm = _tskit.CompressedMatrix(ref_ts_m._ll_tree_sequence)
-    ls_hmm = _tskit.LsHmm(ref_ts_m._ll_tree_sequence, mu, rho, acgt_alleles=True)
-    ls_hmm.forward_matrix(query_h_m.T, fm)
-    ls_hmm.backward_matrix(query_h_m.T, fm.normalisation_factor, bm)
-    # Compute state probability matrix.
-    sm = compute_state_probability_matrix(
-        fm.decode(),
-        bm.decode(),
-        ref_h_m,
-        query_h_m,
-    )
-    # Interpolate allele probabilities.
-    ap = interpolate_allele_probabilities(sm, ref_h_x, genotyped_pos, imputed_pos)
-    # Get imputed alleles.
-    ia = get_map_alleles(ap)
-    return ia