SNP alleles

Documentation

Get the two different alleles of a SNP. The parameter SNP is a list of tuples with genotypes. For example if SNP = [(A,A), (A,G), (G,G), (G,A)] the function returns (A,G)

Parameters

Python list of SNPs:
Character for missing SNP:

<inputs>
<param name="SNP" type="eval" value="" label="Python list of SNPs: "/>
<param name="missing" type="data" value="0" label="Character for missing SNP: "/>
</inputs>

Return

A tuple of the two different alleles that comprise this SNP.

Code

def SNP_alleles(
	SNP = None,
	missing = "0",
):
	allele_1 = None

	for gen in SNP:
		if gen[0] != missing:
			if not allele_1:
				allele_1 = gen[0]
			elif gen[0] != allele_1:
				return (allele_1, gen[0])
		if gen[1] != missing:
			if not allele_1:
				allele_1 = gen[1]
			elif gen[1] != allele_1:
				return (allele_1, gen[1])

	return (allele_1, allele_1)

Unit Tests

def uni1():
	if SNP_alleles([("A","A"), ("A","G"), ("G","G"), ("G","A")]) != ("A", "G"):
		return 'Edit failed to find the alleles of the SNP: [("A","A"), ("A","G"), ("G","G"), ("G","A")]'

	return True

Development Code

def SNP_alleles():
	pass

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