snplib 1.0.7__py3-none-any.whl → 1.0.9__py3-none-any.whl

snplib/statistics/_snphwe.py

@@ -1,132 +1,132 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-import numpy as np
-import pandas as pd
-
-
-def hwe(
-		obs_hets: int | float, obs_hom1: int | float, obs_hom2: int | float
-) -> float:
-	""" Python interpretation hwe - https://github.com/jeremymcrae/snphwe
-
-	:param obs_hets: Number of observed heterozygotes (AB, BA)
-	:param obs_hom1: Number of observed homozygotes1 (AA)
-	:param obs_hom2: Number of observed homozygotes2 (BB)
-	:return: This is where the p-value is returned
-	"""
-
-	obs_hets = round(obs_hets)
-	obs_hom1 = round(obs_hom1)
-	obs_hom2 = round(obs_hom2)
-
-	if obs_hom1 < 0 or obs_hom2 < 0 or obs_hets < 0:
-		raise ValueError("snphwe: negative allele count")
-
-	obs_homr = min(obs_hom1, obs_hom2)
-	obs_homc = max(obs_hom1, obs_hom2)
-
-	rare = 2 * obs_homr + obs_hets
-	genotypes = obs_hets + obs_homc + obs_homr
-
-	if genotypes == 0:
-		raise ValueError("snphwe: zero genotypes")
-
-	probs = np.zeros(round(rare) + 1)
-
-	# get distribution midpoint, but ensure midpoint and rare alleles have
-	# same parity
-	mid = int(rare * (2 * genotypes - rare) / (2 * genotypes))
-	if mid % 2 != rare % 2:
-		mid += 1
-
-	probs[mid] = 1.0
-	_sum = probs[mid]
-
-	curr_homr = (rare - mid) / 2
-	curr_homc = genotypes - mid - curr_homr
-	curr_hets = mid
-	while curr_hets > 1:
-		probs[curr_hets - 2] = (
-			probs[curr_hets] * curr_hets * (curr_hets - 1.0)
-			/ (4.0 * (curr_homr + 1.0) * (curr_homc + 1.0))
-		)
-		_sum += probs[curr_hets - 2]
-
-		# fewer heterozygotes -> add one rare, one common homozygote
-		curr_homr += 1
-		curr_homc += 1
-		curr_hets -= 2
-
-	# calculate probabilities from midpoint up
-	curr_homr = (rare - mid) / 2
-	curr_homc = genotypes - mid - curr_homr
-
-	curr_hets = mid
-	while curr_hets <= rare - 2:
-		probs[curr_hets + 2] = \
-			(probs[curr_hets] * 4.0 * curr_homr * curr_homc
-			 / ((curr_hets + 2.0) * (curr_hets + 1.0)))
-		_sum += probs[curr_hets + 2]
-
-		# add 2 heterozygotes -> subtract one rare, one common homozygote
-		curr_homr -= 1
-		curr_homc -= 1
-		curr_hets += 2
-
-	# p-value calculation for p_hwe
-	target = probs[obs_hets]
-	p_hwe = 0.0
-
-	for p in probs:
-		if p <= target:
-			p_hwe += p / _sum
-
-	return min(1.0, p_hwe)
-
-
-def hwe_test(
-		seq_snp: pd.Series, freq: float, crit_chi2: float = 3.841
-) -> bool:
-	""" The Hardy-Weinberg equilibrium is a principle stating that the genetic
-	variation in a population will remain constant from one generation to the
-	next in the absence of disturbing factors.
-	https://www.nature.com/scitable/definition/hardy-weinberg-equilibrium-122/
-
-	:param seq_snp: SNP sequence
-	:param freq: Allele frequency
-	:param crit_chi2: The critical value for a test ("either / or":
-		observed and expected values are either one way or the other),
-		therefore with degrees of freedom = df = 1 is 3.84 at p = 0.05
-	:return: A decision is returned to exclude or retain the inspected snp
-	"""
-
-	_seq = seq_snp.replace(5, np.nan)
-
-	if _seq.nunique() == 1:
-		return True
-
-	n_genotypes = _seq.count()
-
-	observed = {
-		0: (_seq == 0).sum(),
-		1: (_seq == 1).sum(),
-		2: (_seq == 2).sum()
-	}
-
-	expected = {
-		0: ((1 - freq) ** 2) * n_genotypes,
-		1: (2 * ((1 - freq) * freq)) * n_genotypes,
-		2: (freq ** 2) * n_genotypes
-	}
-
-	chi = sum([
-		((obs - exp) ** 2) / exp
-		for obs, exp in zip(observed.values(), expected.values())
-	])
-
-	if chi > crit_chi2:
-		return False
-	else:
-		return True
+#!/usr/bin/env python
+# coding: utf-8
+__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
+
+import numpy as np
+import pandas as pd
+
+
+def hwe(
+		obs_hets: int | float, obs_hom1: int | float, obs_hom2: int | float
+) -> float:
+	""" Python interpretation hwe - https://github.com/jeremymcrae/snphwe
+
+	:param obs_hets: Number of observed heterozygotes (AB, BA)
+	:param obs_hom1: Number of observed homozygotes1 (AA)
+	:param obs_hom2: Number of observed homozygotes2 (BB)
+	:return: This is where the p-value is returned
+	"""
+
+	obs_hets = round(obs_hets)
+	obs_hom1 = round(obs_hom1)
+	obs_hom2 = round(obs_hom2)
+
+	if obs_hom1 < 0 or obs_hom2 < 0 or obs_hets < 0:
+		raise ValueError("snphwe: negative allele count")
+
+	obs_homr = min(obs_hom1, obs_hom2)
+	obs_homc = max(obs_hom1, obs_hom2)
+
+	rare = 2 * obs_homr + obs_hets
+	genotypes = obs_hets + obs_homc + obs_homr
+
+	if genotypes == 0:
+		raise ValueError("snphwe: zero genotypes")
+
+	probs = np.zeros(round(rare) + 1)
+
+	# get distribution midpoint, but ensure midpoint and rare alleles have
+	# same parity
+	mid = int(rare * (2 * genotypes - rare) / (2 * genotypes))
+	if mid % 2 != rare % 2:
+		mid += 1
+
+	probs[mid] = 1.0
+	_sum = probs[mid]
+
+	curr_homr = (rare - mid) / 2
+	curr_homc = genotypes - mid - curr_homr
+	curr_hets = mid
+	while curr_hets > 1:
+		probs[curr_hets - 2] = (
+			probs[curr_hets] * curr_hets * (curr_hets - 1.0)
+			/ (4.0 * (curr_homr + 1.0) * (curr_homc + 1.0))
+		)
+		_sum += probs[curr_hets - 2]
+
+		# fewer heterozygotes -> add one rare, one common homozygote
+		curr_homr += 1
+		curr_homc += 1
+		curr_hets -= 2
+
+	# calculate probabilities from midpoint up
+	curr_homr = (rare - mid) / 2
+	curr_homc = genotypes - mid - curr_homr
+
+	curr_hets = mid
+	while curr_hets <= rare - 2:
+		probs[curr_hets + 2] = \
+			(probs[curr_hets] * 4.0 * curr_homr * curr_homc
+			 / ((curr_hets + 2.0) * (curr_hets + 1.0)))
+		_sum += probs[curr_hets + 2]
+
+		# add 2 heterozygotes -> subtract one rare, one common homozygote
+		curr_homr -= 1
+		curr_homc -= 1
+		curr_hets += 2
+
+	# p-value calculation for p_hwe
+	target = probs[obs_hets]
+	p_hwe = 0.0
+
+	for p in probs:
+		if p <= target:
+			p_hwe += p / _sum
+
+	return min(1.0, p_hwe)
+
+
+def hwe_test(
+		seq_snp: pd.Series, freq: float, crit_chi2: float = 3.841
+) -> bool:
+	""" The Hardy-Weinberg equilibrium is a principle stating that the genetic
+	variation in a population will remain constant from one generation to the
+	next in the absence of disturbing factors.
+	https://www.nature.com/scitable/definition/hardy-weinberg-equilibrium-122/
+
+	:param seq_snp: SNP sequence
+	:param freq: Allele frequency
+	:param crit_chi2: The critical value for a test ("either / or":
+		observed and expected values are either one way or the other),
+		therefore with degrees of freedom = df = 1 is 3.84 at p = 0.05
+	:return: A decision is returned to exclude or retain the inspected snp
+	"""
+
+	_seq = seq_snp.replace(5, np.nan)
+
+	if _seq.nunique() == 1:
+		return True
+
+	n_genotypes = _seq.count()
+
+	observed = {
+		0: (_seq == 0).sum(),
+		1: (_seq == 1).sum(),
+		2: (_seq == 2).sum()
+	}
+
+	expected = {
+		0: ((1 - freq) ** 2) * n_genotypes,
+		1: (2 * ((1 - freq) * freq)) * n_genotypes,
+		2: (freq ** 2) * n_genotypes
+	}
+
+	chi = sum([
+		((obs - exp) ** 2) / exp
+		for obs, exp in zip(observed.values(), expected.values())
+	])
+
+	if chi > crit_chi2:
+		return False
+	else:
+		return True