def test_GetNewStringMatrix(self):
# create StringMatrix with 3 loci + 1 non-locus keys
A_matrix = StringMatrix(3, ['A', 'B', 'C'], ['foo'])
A_matrix[0, 'B'] = ('B0', 'B0')
A_matrix[1, 'B'] = ('B1', 'B1')
A_matrix[2, 'B'] = ('B3', 'B1')
A_matrix[0, 'A'] = ('A0', 'A0')
A_matrix[1, 'A'] = ('A1', 'A2')
A_matrix[2, 'A'] = ('A0', 'A2')
A_matrix[0, 'C'] = ('C0', 'C0')
A_matrix[1, 'C'] = ('C1', 'C2')
A_matrix[2, 'C'] = ('C2', 'C1')
A_matrix[0, 'foo'] = "bar"
A_matrix[1, 'foo'] = "baz"
A_matrix[2, 'foo'] = "frum"
# get matrix subset
B_matrix = A_matrix.getNewStringMatrix("A:C:foo")
# check new and original matrix columns
assert A_matrix.colList == ['A', 'B', 'C']
assert B_matrix.colList == ['A', 'C']
# check new and original matrix shapes
# note number of cols is twice number of loci + extra column
assert A_matrix.shape == (3, 7)
assert B_matrix.shape == (3, 5)
assert B_matrix['A'] == [['A0', 'A0'], ['A1', 'A2'], ['A0', 'A2']]
assert B_matrix['C'] == [['C0', 'C0'], ['C1', 'C2'], ['C2', 'C1']]
assert B_matrix['foo'] == [['bar'], ['baz'], ['frum']]
def test_GetNewStringMatrix(self):
# create StringMatrix with 3 loci + 1 non-locus keys
A_matrix = StringMatrix(3, ['A', 'B', 'C'], ['foo'])
A_matrix[0, 'B'] = ('B0', 'B0')
A_matrix[1, 'B'] = ('B1', 'B1')
A_matrix[2, 'B'] = ('B3', 'B1')
A_matrix[0, 'A'] = ('A0', 'A0')
A_matrix[1, 'A'] = ('A1', 'A2')
A_matrix[2, 'A'] = ('A0', 'A2')
A_matrix[0, 'C'] = ('C0', 'C0')
A_matrix[1, 'C'] = ('C1', 'C2')
A_matrix[2, 'C'] = ('C2', 'C1')
A_matrix[0, 'foo'] = "bar"
A_matrix[1, 'foo'] = "baz"
A_matrix[2, 'foo'] = "frum"
# get matrix subset
B_matrix = A_matrix.getNewStringMatrix("A:C:foo")
# check new and original matrix columns
assert A_matrix.colList == ['A', 'B', 'C']
assert B_matrix.colList == ['A', 'C']
# check new and original matrix shapes
# note number of cols is twice number of loci + extra column
assert A_matrix.shape == (3, 7)
assert B_matrix.shape == (3, 5)
assert B_matrix['A'] == [['A0', 'A0'], ['A1', 'A2'], ['A0', 'A2']]
assert B_matrix['C'] == [['C0', 'C0'], ['C1', 'C2'], ['C2', 'C1']]
assert B_matrix['foo'] == [['bar'], ['baz'], ['frum']]
def test_ConvertToInt_FlattenCols(self):
geno = StringMatrix(5, ["DRB", "B"])
geno[0, 'DRB'] = ('4', '11')
geno[1, 'DRB'] = ('2', '7')
geno[2, 'DRB'] = ('1', '13')
geno[3, 'DRB'] = ('7', '7')
geno[4, 'DRB'] = ('8', '11')
geno[0, 'B'] = ('62', '61')
geno[1, 'B'] = ('7', '44')
geno[2, 'B'] = ('27', '62')
geno[3, 'B'] = ('7', '44')
geno[4, 'B'] = ('51', '55')
new_geno = geno.convertToInts()
flattened_list = new_geno.flattenCols()
assert flattened_list == [3, 2, 1, 4, 5, 6, 4, 7, 4, 6, 7, 1, 2, 1, 4, 6, 3, 7, 3, 5]
def test_CountPairs_Small(self):
geno = StringMatrix(5, ["DRB", "B"])
geno[0, 'DRB'] = ('4', '11')
geno[1, 'DRB'] = ('2', '7')
geno[2, 'DRB'] = ('1', '13')
geno[3, 'DRB'] = ('7', '7')
geno[4, 'DRB'] = ('8', '11')
geno[0, 'B'] = ('62', '61')
geno[1, 'B'] = ('7', '44')
geno[2, 'B'] = ('27', '62')
geno[3, 'B'] = ('7', '44')
geno[4, 'B'] = ('51', '55')
pairs = geno.countPairs()
max_haps = 2 * sum(pairs)
assert pairs == [2, 2, 2, 1, 2]
assert max_haps == 18
def test_ConvertToInt_FlattenCols(self):
geno = StringMatrix(5, ["DRB", "B"])
geno[0, 'DRB'] = ('4', '11')
geno[1, 'DRB'] = ('2', '7')
geno[2, 'DRB'] = ('1', '13')
geno[3, 'DRB'] = ('7', '7')
geno[4, 'DRB'] = ('8', '11')
geno[0, 'B'] = ('62', '61')
geno[1, 'B'] = ('7', '44')
geno[2, 'B'] = ('27', '62')
geno[3, 'B'] = ('7', '44')
geno[4, 'B'] = ('51', '55')
new_geno = geno.convertToInts()
flattened_list = new_geno.flattenCols()
assert flattened_list == [
3, 2, 1, 4, 5, 6, 4, 7, 4, 6, 7, 1, 2, 1, 4, 6, 3, 7, 3, 5
]
def test_CountPairs_Small(self):
geno = StringMatrix(5, ["DRB", "B"])
geno[0, 'DRB'] = ('4', '11')
geno[1, 'DRB'] = ('2', '7')
geno[2, 'DRB'] = ('1', '13')
geno[3, 'DRB'] = ('7', '7')
geno[4, 'DRB'] = ('8', '11')
geno[0, 'B'] = ('62', '61')
geno[1, 'B'] = ('7', '44')
geno[2, 'B'] = ('27', '62')
geno[3, 'B'] = ('7', '44')
geno[4, 'B'] = ('51', '55')
pairs = geno.countPairs()
max_haps = 2*sum(pairs)
assert pairs == [2, 2, 2, 1, 2]
assert max_haps == 18
def new_matrix():
return StringMatrix(3, ['A', 'B', 'C'])
def test_CountPairs_Large(self):
geno = StringMatrix(45, ['A', 'C', 'B'])
geno[0, 'A'] = ('101', '201')
geno[1, 'A'] = ('210', '3012')
geno[2, 'A'] = ('101', '218')
geno[3, 'A'] = ('2501', '201')
geno[4, 'A'] = ('210', '3204')
geno[5, 'A'] = ('3012', '3204')
geno[6, 'A'] = ('2501', '3204')
geno[7, 'A'] = ('6814', '201')
geno[8, 'A'] = ('201', '201')
geno[9, 'A'] = ('3204', '101')
geno[10, 'A'] = ('6901', '210')
geno[11, 'A'] = ('210', '3012')
geno[12, 'A'] = ('101', '218')
geno[13, 'A'] = ('101', '201')
geno[14, 'A'] = ('210', '3012')
geno[15, 'A'] = ('101', '218')
geno[16, 'A'] = ('101', '218')
geno[17, 'A'] = ('2501', '201')
geno[18, 'A'] = ('201', '201')
geno[19, 'A'] = ('3012', '2501')
geno[20, 'A'] = ('218', '6814')
geno[21, 'A'] = ('201', '201')
geno[22, 'A'] = ('3204', '2501')
geno[23, 'A'] = ('218', '218')
geno[24, 'A'] = ('3012', '3012')
geno[25, 'A'] = ('101', '2501')
geno[26, 'A'] = ('101', '210')
geno[27, 'A'] = ('210', '3012')
geno[28, 'A'] = ('101', '2501')
geno[29, 'A'] = ('3204', '6814')
geno[30, 'A'] = ('201', '201')
geno[31, 'A'] = ('201', '3204')
geno[32, 'A'] = ('101', '6901')
geno[33, 'A'] = ('210', '210')
geno[34, 'A'] = ('3012', '6901')
geno[35, 'A'] = ('218', '2501')
geno[36, 'A'] = ('101', '2501')
geno[37, 'A'] = ('7403', '201')
geno[38, 'A'] = ('2501', '3012')
geno[39, 'A'] = ('201', '201')
geno[40, 'A'] = ('3012', '3012')
geno[41, 'A'] = ('3204', '2501')
geno[42, 'A'] = ('201', '201')
geno[43, 'A'] = ('3012', '3012')
geno[44, 'A'] = ('6901', '218')
geno[0, 'C'] = ('307', '605')
geno[1, 'C'] = ('712', '102')
geno[2, 'C'] = ('804', '1202')
geno[3, 'C'] = ('1507', '307')
geno[4, 'C'] = ('1801', '102')
geno[5, 'C'] = ('1507', '605')
geno[6, 'C'] = ('307', '307')
geno[7, 'C'] = ('102', '712')
geno[8, 'C'] = ('1202', '2025')
geno[9, 'C'] = ('307', '605')
geno[10, 'C'] = ('102', '102')
geno[11, 'C'] = ('1202', '1202')
geno[12, 'C'] = ('307', '307')
geno[13, 'C'] = ('102', '102')
geno[14, 'C'] = ('1507', '307')
geno[15, 'C'] = ('307', '712')
geno[16, 'C'] = ('102', '102')
geno[17, 'C'] = ('1202', '1507')
geno[18, 'C'] = ('307', '307')
geno[19, 'C'] = ('102', '102')
geno[20, 'C'] = ('307', '307')
geno[21, 'C'] = ('1208', '307')
geno[22, 'C'] = ('307', '102')
geno[23, 'C'] = ('102', '307')
geno[24, 'C'] = ('605', '307')
geno[25, 'C'] = ('605', '605')
geno[26, 'C'] = ('1202', '1507')
geno[27, 'C'] = ('307', '307')
geno[28, 'C'] = ('102', '102')
geno[29, 'C'] = ('605', '1202')
geno[30, 'C'] = ('307', '307')
geno[31, 'C'] = ('712', '102')
geno[32, 'C'] = ('2025', '102')
geno[33, 'C'] = ('605', '102')
geno[34, 'C'] = ('3021', '605')
geno[35, 'C'] = ('605', '605')
geno[36, 'C'] = ('501', '408')
geno[37, 'C'] = ('605', '307')
geno[38, 'C'] = ('712', '3021')
geno[39, 'C'] = ('403', '307')
geno[40, 'C'] = ('307', '605')
geno[41, 'C'] = ('605', '1202')
geno[42, 'C'] = ('307', '307')
geno[43, 'C'] = ('102', '102')
geno[44, 'C'] = ('102', '307')
geno[0, 'B'] = ('307', '605')
geno[1, 'B'] = ('712', '102')
geno[2, 'B'] = ('804', '1202')
geno[3, 'B'] = ('1507', '307')
geno[4, 'B'] = ('1801', '102')
geno[5, 'B'] = ('1507', '605')
geno[6, 'B'] = ('307', '307')
geno[7, 'B'] = ('102', '712')
geno[8, 'B'] = ('1202', '2025')
geno[9, 'B'] = ('307', '605')
geno[10, 'B'] = ('102', '102')
geno[11, 'B'] = ('1202', '1202')
geno[12, 'B'] = ('307', '307')
geno[13, 'B'] = ('102', '102')
geno[14, 'B'] = ('1507', '307')
geno[15, 'B'] = ('307', '712')
geno[16, 'B'] = ('102', '102')
geno[17, 'B'] = ('1202', '1507')
geno[18, 'B'] = ('307', '307')
geno[19, 'B'] = ('102', '102')
geno[20, 'B'] = ('307', '307')
geno[21, 'B'] = ('1208', '307')
geno[22, 'B'] = ('307', '102')
geno[23, 'B'] = ('102', '307')
geno[24, 'B'] = ('605', '307')
geno[25, 'B'] = ('605', '605')
geno[26, 'B'] = ('1202', '1507')
geno[27, 'B'] = ('307', '307')
geno[28, 'B'] = ('102', '102')
geno[29, 'B'] = ('605', '1202')
geno[30, 'B'] = ('307', '307')
geno[31, 'B'] = ('712', '102')
geno[32, 'B'] = ('2025', '102')
geno[33, 'B'] = ('605', '102')
geno[34, 'B'] = ('3021', '605')
geno[35, 'B'] = ('605', '605')
geno[36, 'B'] = ('501', '408')
geno[37, 'B'] = ('605', '307')
geno[38, 'B'] = ('712', '3021')
geno[39, 'B'] = ('403', '307')
geno[40, 'B'] = ('307', '605')
geno[41, 'B'] = ('605', '1202')
geno[42, 'B'] = ('307', '307')
geno[43, 'B'] = ('102', '102')
geno[44, 'B'] = ('102', '307')
pairs = geno.countPairs()
max_haps = 2 * sum(pairs)
assert pairs == [
4, 4, 4, 4, 4, 4, 1, 4, 2, 4, 1, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 2,
4, 2, 2, 1, 4, 1, 1, 4, 1, 4, 4, 2, 4, 1, 4, 4, 4, 2, 2, 4, 1, 1, 4
]
assert max_haps == 236
# geno = hla.demo[1:5,c(21:24)]
# label <-c("DRB","B")
# save.em <- haplo.em(geno=geno, locus.label=label, control=control)
# R geno matrix looks like this:
# DRB.a1 DRB.a2 B.a1 B.a2
# 4 11 62 61
# 2 7 7 44
# 1 13 27 62
# 7 7 7 44
# 8 11 51 55
# so we set StringMatrix to be:
geno = StringMatrix(5, ["DRB", "B"])
geno[0, 'DRB'] = ('4', '11')
geno[1, 'DRB'] = ('2', '7')
geno[2, 'DRB'] = ('1', '13')
geno[3, 'DRB'] = ('7', '7')
geno[4, 'DRB'] = ('8', '11')
geno[0, 'B'] = ('62', '61')
geno[1, 'B'] = ('7', '44')
geno[2, 'B'] = ('27', '62')
geno[3, 'B'] = ('7', '44')
geno[4, 'B'] = ('51', '55')
# set all the control parameters
# possibly move this into the .ini file eventually?
control = {
'max_iter': 5000,
def test_Haplostats_PyPopStringMatrix():
"""
This is the same numerical example as test_Haplostats_Simple()
except we are setting up via PyPop StringMatrix, and letting the class
handle all the translation into the low-level variables for the wrapper
"""
from PyPop.Utils import StringMatrix
from PyPop.Haplo import Haplostats
import numpy
import numpy.testing
control = {
'max_iter': 5000,
'min_posterior': 0.000000001,
'tol': 0.00001,
'insert_batch_size': 2,
'random_start': 0,
'verbose': 0,
'max_haps_limit': 10000
}
geno = StringMatrix(5, ["DRB", "B"])
geno[0, 'DRB'] = ('4', '11')
geno[1, 'DRB'] = ('2', '7')
geno[2, 'DRB'] = ('1', '13')
geno[3, 'DRB'] = ('7', '7')
geno[4, 'DRB'] = ('8', '11')
geno[0, 'B'] = ('62', '61')
geno[1, 'B'] = ('7', '44')
geno[2, 'B'] = ('27', '62')
geno[3, 'B'] = ('7', '44')
geno[4, 'B'] = ('51', '55')
haplo = Haplostats(geno)
converge, lnlike, n_u_hap, n_hap_pairs, hap_prob, u_hap, u_hap_code, subj_id, post, hap1_code, hap2_code, haplotype, dprime, Wn, ALD_1_2, ALD_2_1 = \
haplo.estHaplotypes(weight=None, control=control, numInitCond=1, testMode=True)
assert converge == 1
assert lnlike == -20.42316124449607
assert n_u_hap == 16
assert n_hap_pairs == 9
assert hap_prob == [
0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.15, 0.15, 0.05, 0.05, 0.05, 0.05,
0.05, 0.05, 0.05, 0.05
]
assert u_hap == [
1, 2, 1, 7, 2, 1, 2, 3, 3, 6, 3, 7, 4, 1, 4, 3, 5, 4, 5, 5, 6, 4, 6, 5,
6, 6, 6, 7, 7, 2, 7, 7
]
assert u_hap_code == [
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16
]
assert subj_id == [1, 1, 2, 2, 3, 3, 4, 5, 5]
assert post == [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 1.0, 0.5, 0.5]
# FIXME: disabled for the moment, apparently platform-dependent (see #28)
# assert hap1_code == [6, 5, 3, 4, 1, 2, 7, 9, 10]
# assert hap2_code == [13, 14, 8, 7, 16, 15, 8, 12, 11]
numpy.testing.assert_array_equal(
haplotype,
numpy.array([['1', '27'], ['1', '62'], ['2', '7'], ['2', '44'],
['4', '61'], ['4', '62'], ['7', '7'], ['7', '44'],
['8', '51'], ['8', '55'], ['11', '51'], ['11', '55'],
['11', '61'], ['11', '62'], ['13', '27'], ['13', '62']]))
# FIXME: check!
assert dprime == approx(0.791865079365)
assert Wn == approx(0.586301969978)
assert ALD_1_2 == approx(0.624695047554)
assert ALD_2_1 == approx(0.587569651393)
# try again with same input data, but running with more iterations, to test whether the loop is behaving deterministically
# this gives a different loglikelihood and completely different set of haplotypes
converge, lnlike, n_u_hap, n_hap_pairs, hap_prob, u_hap, u_hap_code, subj_id, post, hap1_code, hap2_code, haplotype, dprime, Wn, ALD_1_2, ALD_2_1 = \
haplo.estHaplotypes(weight=None, control=control, numInitCond=10, testMode=True)
assert converge == 1
assert lnlike == -18.173826527916734
assert n_u_hap == 10
assert n_hap_pairs == 6
assert_array_almost_equal(hap_prob, [
0.1, 5.862016163766863e-07, 0.09999941379838362, 0.1,
0.19999941379838362, 0.10000058620161638, 0.1, 0.1, 0.1, 0.1
])
assert u_hap == [
1, 2, 2, 1, 2, 3, 3, 6, 4, 1, 4, 3, 5, 5, 6, 4, 6, 7, 7, 7
]
assert u_hap_code == [1, 3, 4, 5, 7, 8, 10, 11, 14, 16]
assert subj_id == [1, 2, 2, 3, 4, 5]
assert_array_almost_equal(
post, [1.0, 5.862016163766862e-06, 0.9999941379838362, 1.0, 1.0, 1.0])
numpy.testing.assert_array_equal(
haplotype,
numpy.array([['1', '27'], ['2', '7'], ['2', '44'], ['4', '61'],
['7', '7'], ['7', '44'], ['8', '55'], ['11', '51'],
['11', '62'], ['13', '62']]))
# FIXME: check!
assert dprime == approx(0.932142124391)
assert Wn == approx(0.874006628251)
assert ALD_1_2 == approx(0.86953788372)
assert ALD_2_1 == approx(0.849835490713)
#!/usr/bin/env python
import os.path
import sys
import string
import numpy
DIR = os.path.abspath(os.path.dirname(__file__))
sys.path.insert(0, os.path.join(DIR, '..'))
from PyPop.Utils import StringMatrix
from PyPop.Haplo import Haplostats
# matching USAFEL-UchiTelle.pop example
geno = StringMatrix(45, ['A', 'C', 'B'])
geno[0, 'A'] = ('101', '201')
geno[1, 'A'] = ('210', '3012')
geno[2, 'A'] = ('101', '218')
geno[3, 'A'] = ('2501', '201')
geno[4, 'A'] = ('210', '3204')
geno[5, 'A'] = ('3012', '3204')
geno[6, 'A'] = ('2501', '3204')
geno[7, 'A'] = ('6814', '201')
geno[8, 'A'] = ('201', '201')
geno[9, 'A'] = ('3204', '101')
geno[10, 'A'] = ('6901', '210')
geno[11, 'A'] = ('210', '3012')
geno[12, 'A'] = ('101', '218')
geno[13, 'A'] = ('101', '201')
geno[14, 'A'] = ('210', '3012')
geno[15, 'A'] = ('101', '218')
def test_CountPairs_Large(self):
geno = StringMatrix(45, ['A', 'C', 'B'])
geno[ 0, 'A'] = ( '101', '201')
geno[ 1, 'A'] = ( '210', '3012')
geno[ 2, 'A'] = ( '101', '218')
geno[ 3, 'A'] = ( '2501', '201')
geno[ 4, 'A'] = ( '210', '3204')
geno[ 5, 'A'] = ( '3012', '3204')
geno[ 6, 'A'] = ( '2501', '3204')
geno[ 7, 'A'] = ( '6814', '201')
geno[ 8, 'A'] = ( '201', '201')
geno[ 9, 'A'] = ( '3204', '101')
geno[10, 'A'] = ( '6901', '210')
geno[11, 'A'] = ( '210', '3012')
geno[12, 'A'] = ( '101', '218')
geno[13, 'A'] = ( '101', '201')
geno[14, 'A'] = ( '210', '3012')
geno[15, 'A'] = ( '101', '218')
geno[16, 'A'] = ( '101', '218')
geno[17, 'A'] = ( '2501', '201')
geno[18, 'A'] = ( '201', '201')
geno[19, 'A'] = ( '3012', '2501')
geno[20, 'A'] = ( '218', '6814')
geno[21, 'A'] = ( '201', '201')
geno[22, 'A'] = ( '3204', '2501')
geno[23, 'A'] = ( '218', '218')
geno[24, 'A'] = ( '3012', '3012')
geno[25, 'A'] = ( '101', '2501')
geno[26, 'A'] = ( '101', '210')
geno[27, 'A'] = ( '210', '3012')
geno[28, 'A'] = ( '101', '2501')
geno[29, 'A'] = ( '3204', '6814')
geno[30, 'A'] = ( '201', '201')
geno[31, 'A'] = ( '201', '3204')
geno[32, 'A'] = ( '101', '6901')
geno[33, 'A'] = ( '210', '210')
geno[34, 'A'] = ( '3012', '6901')
geno[35, 'A'] = ( '218', '2501')
geno[36, 'A'] = ( '101', '2501')
geno[37, 'A'] = ( '7403', '201')
geno[38, 'A'] = ( '2501', '3012')
geno[39, 'A'] = ( '201', '201')
geno[40, 'A'] = ( '3012', '3012')
geno[41, 'A'] = ( '3204', '2501')
geno[42, 'A'] = ( '201', '201')
geno[43, 'A'] = ( '3012', '3012')
geno[44, 'A'] = ( '6901', '218')
geno[ 0, 'C'] = ( '307', '605')
geno[ 1, 'C'] = ( '712', '102')
geno[ 2, 'C'] = ( '804', '1202')
geno[ 3, 'C'] = ( '1507', '307')
geno[ 4, 'C'] = ( '1801', '102')
geno[ 5, 'C'] = ( '1507', '605')
geno[ 6, 'C'] = ( '307', '307')
geno[ 7, 'C'] = ( '102', '712')
geno[ 8, 'C'] = ( '1202', '2025')
geno[ 9, 'C'] = ( '307', '605')
geno[10, 'C'] = ( '102', '102')
geno[11, 'C'] = ( '1202', '1202')
geno[12, 'C'] = ( '307', '307')
geno[13, 'C'] = ( '102', '102')
geno[14, 'C'] = ( '1507', '307')
geno[15, 'C'] = ( '307', '712')
geno[16, 'C'] = ( '102', '102')
geno[17, 'C'] = ( '1202', '1507')
geno[18, 'C'] = ( '307', '307')
geno[19, 'C'] = ( '102', '102')
geno[20, 'C'] = ( '307', '307')
geno[21, 'C'] = ( '1208', '307')
geno[22, 'C'] = ( '307', '102')
geno[23, 'C'] = ( '102', '307')
geno[24, 'C'] = ( '605', '307')
geno[25, 'C'] = ( '605', '605')
geno[26, 'C'] = ( '1202', '1507')
geno[27, 'C'] = ( '307', '307')
geno[28, 'C'] = ( '102', '102')
geno[29, 'C'] = ( '605', '1202')
geno[30, 'C'] = ( '307', '307')
geno[31, 'C'] = ( '712', '102')
geno[32, 'C'] = ( '2025', '102')
geno[33, 'C'] = ( '605', '102')
geno[34, 'C'] = ( '3021', '605')
geno[35, 'C'] = ( '605', '605')
geno[36, 'C'] = ( '501', '408')
geno[37, 'C'] = ( '605', '307')
geno[38, 'C'] = ( '712', '3021')
geno[39, 'C'] = ( '403', '307')
geno[40, 'C'] = ( '307', '605')
geno[41, 'C'] = ( '605', '1202')
geno[42, 'C'] = ( '307', '307')
geno[43, 'C'] = ( '102', '102')
geno[44, 'C'] = ( '102', '307')
geno[ 0, 'B'] = ( '307', '605')
geno[ 1, 'B'] = ( '712', '102')
geno[ 2, 'B'] = ( '804', '1202')
geno[ 3, 'B'] = ( '1507', '307')
geno[ 4, 'B'] = ( '1801', '102')
geno[ 5, 'B'] = ( '1507', '605')
geno[ 6, 'B'] = ( '307', '307')
geno[ 7, 'B'] = ( '102', '712')
geno[ 8, 'B'] = ( '1202', '2025')
geno[ 9, 'B'] = ( '307', '605')
geno[10, 'B'] = ( '102', '102')
geno[11, 'B'] = ( '1202', '1202')
geno[12, 'B'] = ( '307', '307')
geno[13, 'B'] = ( '102', '102')
geno[14, 'B'] = ( '1507', '307')
geno[15, 'B'] = ( '307', '712')
geno[16, 'B'] = ( '102', '102')
geno[17, 'B'] = ( '1202', '1507')
geno[18, 'B'] = ( '307', '307')
geno[19, 'B'] = ( '102', '102')
geno[20, 'B'] = ( '307', '307')
geno[21, 'B'] = ( '1208', '307')
geno[22, 'B'] = ( '307', '102')
geno[23, 'B'] = ( '102', '307')
geno[24, 'B'] = ( '605', '307')
geno[25, 'B'] = ( '605', '605')
geno[26, 'B'] = ( '1202', '1507')
geno[27, 'B'] = ( '307', '307')
geno[28, 'B'] = ( '102', '102')
geno[29, 'B'] = ( '605', '1202')
geno[30, 'B'] = ( '307', '307')
geno[31, 'B'] = ( '712', '102')
geno[32, 'B'] = ( '2025', '102')
geno[33, 'B'] = ( '605', '102')
geno[34, 'B'] = ( '3021', '605')
geno[35, 'B'] = ( '605', '605')
geno[36, 'B'] = ( '501', '408')
geno[37, 'B'] = ( '605', '307')
geno[38, 'B'] = ( '712', '3021')
geno[39, 'B'] = ( '403', '307')
geno[40, 'B'] = ( '307', '605')
geno[41, 'B'] = ( '605', '1202')
geno[42, 'B'] = ( '307', '307')
geno[43, 'B'] = ( '102', '102')
geno[44, 'B'] = ( '102', '307')
pairs = geno.countPairs()
max_haps = 2*sum(pairs)
assert pairs == [4, 4, 4, 4, 4, 4, 1, 4, 2, 4, 1, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 2, 4, 2, 2, 1, 4, 1, 1, 4, 1, 4, 4, 2, 4, 1, 4, 4, 4, 2, 2, 4, 1, 1, 4]
assert max_haps == 236