def caffeine_metabolism(genome):
"""Caffeine metabolism."""
assert_european(genome)
return unphased_match(
genome.rs762551,
{"AA": "Fast metabolizer", "AC": "Slow metabolizer", "CC": "Slow metabolizer", None: "Unable to determine"},
)
def exfoliation_glaucoma(genome):
"""Exfoliation glaucoma."""
assert_european(genome)
OR = unphased_match(genome.rs2165241, {
"CT": 0.79,
})
raise NotImplementedError()
def biological_age(genome):
"""Biological aging (telomere lengths)."""
assert_european(genome)
ages = {
"rs10936599": {"TT": 7.82, "CT": 3.91, "CC": 0, None: 0},
"rs2736100": {"AA": 3.14, "AC": 0, "CC": -3.14, None: 0},
"rs9420907": {"AA": 0, "AC": -2.76, "CC": -5.52, None: 0},
"rs755017": {"AA": 0, "AG": -2.47, "GG": -4.94, None: 0},
"rs11100479": {"CC": 5.98, "CT": -2.99, "TT": 0, None: 0},
"rs10165485": {"TT": 0, "CT": -2.23, "CC": -4.46, None: 0},
}
age = [unphased_match(genome[rsid], t) for (rsid, t) in ages.items()]
def qual(age):
if age <= 0:
return "younger"
elif age > 0:
return "older"
msg = "From %.1f years %s to %.1f years %s than actual age\n" % (
abs(min(age)),
qual(min(age)),
abs(max(age)),
qual(max(age)),
)
msg += "The sum is %.1f years %s, compared to actual age" % (abs(sum(age)), qual(sum(age)))
return msg
def hair_curl(genome):
assert_european(genome)
return unphased_match(
genome.rs17646946, {
"AA": "Straighter hair on average",
"AG": "Straighter hair on average",
"GG": "Slightly curlier hair on average"
})
def birth_weight(genome):
"""Birth weight."""
assert_european(genome)
weights = {
"rs7903146": {"TT": 0, "CT": -30, "CC": -60, None: 0},
"rs1799884": {"TT": +54, "CT": +27, "CC": 0, None: 0},
}
weight = [unphased_match(genome[rsid], w) for (rsid, w) in weights.items()]
return "From %.1fg to %.1fg (sum: %.1fg) compared to typical weight" % (min(weight), max(weight), sum(weight))
def biological_age(genome):
"""Biological aging (telomere lengths)."""
assert_european(genome)
ages = {
"rs10936599": {
"TT": 7.82,
"CT": 3.91,
"CC": 0,
None: 0
},
"rs2736100": {
"AA": 3.14,
"AC": 0,
"CC": -3.14,
None: 0
},
"rs9420907": {
"AA": 0,
"AC": -2.76,
"CC": -5.52,
None: 0
},
"rs755017": {
"AA": 0,
"AG": -2.47,
"GG": -4.94,
None: 0
},
"rs11100479": {
"CC": 5.98,
"CT": -2.99,
"TT": 0,
None: 0
},
"rs10165485": {
"TT": 0,
"CT": -2.23,
"CC": -4.46,
None: 0
},
}
age = [unphased_match(genome[rsid], t) for (rsid, t) in ages.items()]
def qual(age):
if age <= 0:
return "younger"
elif age > 0:
return "older"
msg = "From %.1f years %s to %.1f years %s than actual age\n" % (abs(
min(age)), qual(min(age)), abs(max(age)), qual(max(age)))
msg += "The sum is %.1f years %s, compared to actual age" % (abs(
sum(age)), qual(sum(age)))
return msg
def hair_curl(genome):
assert_european(genome)
return unphased_match(
genome.rs17646946,
{
"AA": "Straighter hair on average",
"AG": "Straighter hair on average",
"GG": "Slightly curlier hair on average",
},
)
def caffeine_metabolism(genome):
"""Caffeine metabolism."""
assert_european(genome)
return unphased_match(
genome.rs762551, {
"AA": "Fast metabolizer",
"AC": "Slow metabolizer",
"CC": "Slow metabolizer",
None: "Unable to determine"
})
def eye_color(genome):
"Eye color."
assert_european(genome)
return unphased_match(
genome.rs12913832, {
"AA": "Brown eyes, although 14% have green and 1% have blue",
"AG": "Most likely brown or green, but 7% have blue",
"GG": "Most likely blue, but 30% have green and 1% brown",
None: "Unable to determine"
})
def blood_glucose(genome):
"""Blood glucose."""
assert_european(genome)
return unphased_match(
genome.rs560887, {
"CC": "Average fasting plasma glucose levels of 5.18mmol/L",
"CT": "Average fasting plasma glucose levels of 5.12mmol/L",
"TT": "Average fasting plasma glucose levels of 5.06mmol/L",
None: "Unable to determine"
})
def aspargus_detection(genome):
"""Aspargus metabolite detection."""
assert_european(genome)
return unphased_match(
genome.rs4481887, {
"AA": "Higher odds of smelling aspargus in urine",
"AG": "Medium odds of smelling aspargus in urine",
"GG": "Typical odds of smelling aspargus in urine",
None: "Unable to determine"
})
def heroin_addiction(genome):
"""Heroin addiction."""
assert_european(genome)
return unphased_match(
genome.rs1799971, {
"AA": "Typical odds of addiction",
"AG": "Higher odds of addiction",
"GG": "Higher odds of addiction",
None: "Unable to determine"
})
def smoking_behaviour(genome):
"""Smoking behaviour."""
assert_european(genome)
return unphased_match(
genome.rs1051730, {
"AA": "Likely to smoke more than average",
"AG": "Likely to smoke a little bit more than average",
"GG": "Likely to smoke typical amount of cigarettes per day",
None: "Unable to determine"
})
def aspargus_detection(genome):
"""Aspargus metabolite detection."""
assert_european(genome)
return unphased_match(
genome.rs4481887,
{
"AA": "Higher odds of smelling aspargus in urine",
"AG": "Medium odds of smelling aspargus in urine",
"GG": "Typical odds of smelling aspargus in urine",
None: "Unable to determine",
},
)
def heroin_addiction(genome):
"""Heroin addiction."""
assert_european(genome)
return unphased_match(
genome.rs1799971,
{
"AA": "Typical odds of addiction",
"AG": "Higher odds of addiction",
"GG": "Higher odds of addiction",
None: "Unable to determine",
},
)
def smoking_behaviour(genome):
"""Smoking behaviour."""
assert_european(genome)
return unphased_match(
genome.rs1051730,
{
"AA": "Likely to smoke more than average",
"AG": "Likely to smoke a little bit more than average",
"GG": "Likely to smoke typical amount of cigarettes per day",
None: "Unable to determine",
},
)
def blood_glucose(genome):
"""Blood glucose."""
assert_european(genome)
return unphased_match(
genome.rs560887,
{
"CC": "Average fasting plasma glucose levels of 5.18mmol/L",
"CT": "Average fasting plasma glucose levels of 5.12mmol/L",
"TT": "Average fasting plasma glucose levels of 5.06mmol/L",
None: "Unable to determine",
},
)
def eye_color(genome):
"Eye color."
assert_european(genome)
return unphased_match(
genome.rs12913832,
{
"AA": "Brown eyes, although 14% have green and 1% have blue",
"AG": "Most likely brown or green, but 7% have blue",
"GG": "Most likely blue, but 30% have green and 1% brown",
None: "Unable to determine",
},
)
def breastfeeding_iq(genome):
"Breastfeeding and IQ."
assert_european(genome)
s = ""
if "C" in genome.rs174575:
s += "Being breastfed raised subjects' IQ by 6-7 points on average (rs174575)\n"
else:
s += "Little to no effect of being breastfed on IQ (rs174575)\n"
if "A" in genome.rs1535:
s += "Being breastfed raised subjects' IQ by 4-5 points on average (rs1535)\n"
else:
s += "Little or no effect of being breastfed on IQ (rs1535)\n"
return s
def birth_weight(genome):
"""Birth weight."""
assert_european(genome)
weights = {
"rs7903146": {
"TT": 0,
"CT": -30,
"CC": -60,
None: 0
},
"rs1799884": {
"TT": +54,
"CT": +27,
"CC": 0,
None: 0
},
}
weight = [unphased_match(genome[rsid], w) for (rsid, w) in weights.items()]
return "From %.1fg to %.1fg (sum: %.1fg) compared to typical weight" % (
min(weight), max(weight), sum(weight))
def migraines(genome):
"""Migranes."""
assert_european(genome)
s = []
s.append(unphased_match(genome.rs2651899, {
"CC": "Slightly higher odds of migraines",
"CT": "Typical odds of migraines",
"TT": "Slightly lower odds of migraines",
None: "Unable to determine"}))
s.append(unphased_match(genome.rs10166942, {
"TT": "Typical odds of migraines",
"CT": "Slightly lower odds of migraines",
"CC": "Slightly lower odds of migraines",
None: "Unable to determine"}))
s.append(unphased_match(genome.rs11172113, {
"TT": "Slightly higher odds of migraines",
"CT": "Typical odds of migraines",
"CC": "Slightly lower odds of migraines",
None: "Unable to determine"}))
return "\n".join(s)
