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genetic-trait-detector.py
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"""
genetic trait detection library
"""
import sys
from colored import fg, attr
class Rsid:
"""genetic rsid detector class"""
def __init__(
self,
rsid: str,
alleles: tuple | str,
association: str,
) -> None:
"""constructor"""
self.rsid = rsid
self.alleles = alleles if isinstance(alleles, tuple) else (alleles,)
self.association = association
def detect(self, line: str) -> bool:
"""detect this rsid in the given line of dna data"""
return self.rsid in line and any(y in line for y in self.allele_match_set)
def __str__(self) -> str:
"""string representation"""
return f"<Rsid[{self.rsid}]({self.association})>"
def __repr__(self) -> str:
"""repl representation"""
return self.__str__()
@property
def single_allele(self) -> bool:
"""if this is a single allele match"""
return len(self.alleles) == 1
@property
def allele_match_set(self) -> tuple:
"""form a set of different formats of alleles"""
def _set(allele: str) -> tuple:
"""form a set of allele formats"""
if ";" in allele:
a0, a1 = allele.upper().split(";")
return (f"{a0} {a1}", f"{a0}|{a1}", f"{a0}{a1}")
return (allele,)
tuples = ()
for allele in self.alleles:
tuples += _set(allele)
return tuples
@property
def url(self) -> str:
"""return the url to snpedia"""
return f"https://www.snpedia.com/index.php/{self.rsid}"
@property
def info(self) -> str:
"""return an informational string about this rsid when detected"""
allele = (
f"with the genotype of ({self.alleles[0]}) " if self.single_allele else ""
)
return (
f"You have a trait which is associated with {trait_colors[self.association]}{self.association}{attr(0)} | "
f"{self.rsid} {allele}{self.url}"
)
class Trait:
"""traits enum class"""
alzheimers = "Alzheimer's Disease"
autism = "Autism"
bipolar_disorder = "Bipolar Disorder"
immunity = "Immunity"
intelligence = "Intelligence"
longevity = "Longevity"
metabolism = "Metabolism"
muscular_performance = "Muscular Performance"
ocd = "OCD"
schizophrenia = "Schizophrenia"
eyes = "Eyes"
hair = "Hair"
trait_colors = {
Trait.alzheimers: fg('light_yellow'),
Trait.autism: fg('green'),
Trait.bipolar_disorder: fg('yellow'),
Trait.immunity: fg('red'),
Trait.intelligence: fg('cyan'),
Trait.longevity: fg('blue'),
Trait.metabolism: fg('dark_turquoise'),
Trait.muscular_performance: fg('light_green'),
Trait.ocd: fg('light_magenta'),
Trait.schizophrenia: fg('magenta'),
Trait.eyes: fg('light_blue'),
Trait.hair: fg('light_red'),
}
_RSIDS = [
("rs1006737", "A;A", Trait.bipolar_disorder),
("rs4027132", "A;A", Trait.bipolar_disorder),
("rs7570682", "A;A", Trait.bipolar_disorder),
("rs1375144", "C;C", Trait.bipolar_disorder),
("rs683395", "C;T", Trait.bipolar_disorder),
("rs2609653", "C;T", Trait.bipolar_disorder),
("rs10982256", "C;C", Trait.bipolar_disorder),
("rs11622475", "C;C", Trait.bipolar_disorder),
("rs1344484", "T;T", Trait.bipolar_disorder),
("rs2953145", "C;G", Trait.bipolar_disorder),
("rs420259", "T;T", Trait.bipolar_disorder),
("rs4276227", "C;C", Trait.bipolar_disorder),
("rs4027132", "A;G", Trait.bipolar_disorder),
("rs2609653", "C;C", Trait.bipolar_disorder),
("rs2953145", "G;G", Trait.bipolar_disorder),
("rs429358", "C;C", Trait.alzheimers),
("rs145999145", "A;A", Trait.alzheimers),
("rs908832", "A;A", Trait.alzheimers),
("rs63750847", "A;A", Trait.alzheimers),
("rs429358", "C;T", Trait.alzheimers),
("rs145999145", "A;G", Trait.alzheimers),
("rs63750847", "A;G", Trait.alzheimers),
("rs1858830", "C;C", Trait.autism),
("rs2710102", "C;C", Trait.autism),
("rs7794745", "A;T", Trait.autism),
("rs1322784", "C;C", Trait.autism),
("rs1322784", "C;T", Trait.autism),
("rs1322784", "T;T", Trait.autism),
("rs265981", "A;G", Trait.autism),
("rs4532", "C;T", Trait.autism),
("rs686", "A;G", Trait.autism),
("rs1143674", "A;A", Trait.autism),
("rs6807362", "C;C", Trait.autism),
("rs757972971", "A;A", Trait.autism),
("rs2217262", "A;A", Trait.autism),
("rs6766410", "A;A", Trait.autism),
("rs6766410", "A;C", Trait.autism),
("rs6766410", "C;C", Trait.autism),
("rs1445442", "A;A", Trait.autism),
("rs1445442", "A;G", Trait.autism),
("rs1445442", "G;G", Trait.autism),
("rs2421826", "C;T", Trait.autism),
("rs2421826", "T;T", Trait.autism),
("rs2421826", "C;C", Trait.autism),
("rs1358054", "G;G", Trait.autism),
("rs1358054", "G;T", Trait.autism),
("rs1358054", "T;T", Trait.autism),
("rs536861", "A;A", Trait.autism),
("rs536861", "A;C", Trait.autism),
("rs536861", "C;C", Trait.autism),
("rs722628", "A;A", Trait.autism),
("rs722628", "A;G", Trait.autism),
("rs722628", "G;G", Trait.autism),
("rs1858830", "C;G", Trait.autism),
("rs2710102", "G;G", Trait.autism),
("rs7794745", "T;T", Trait.autism),
("rs265981", "G;G", Trait.autism),
("rs4532", "T;T", Trait.autism),
("rs686", "A;A", Trait.autism),
("rs1143674", "A;A", Trait.autism),
("rs757972971", "A;A", Trait.autism),
("rs27388", "A;A", Trait.schizophrenia),
("rs2270641", "G;G", Trait.schizophrenia),
("rs4129148", "C;C", Trait.schizophrenia),
("rs28694718", "A;A", Trait.schizophrenia),
("rs6422441", "C;C", Trait.schizophrenia),
("rs28414810", "C;C", Trait.schizophrenia),
("rs6603272", "G;G", Trait.schizophrenia),
("rs17883192", "C;C", Trait.schizophrenia),
("rs165599", "G;G", Trait.schizophrenia),
("rs27388", "A;G", Trait.schizophrenia),
("rs4129148", "C;G", Trait.schizophrenia),
("rs28694718", "A;G", Trait.schizophrenia),
("rs6422441", "C;T", Trait.schizophrenia),
("rs28414810", "C;G", Trait.schizophrenia),
("rs6603272", "G;T", Trait.schizophrenia),
("rs17883192", "C;G", Trait.schizophrenia),
("rs3758391", "C;T", Trait.longevity),
("rs5882", "A;A", Trait.longevity),
("rs1042522", "C;C", Trait.longevity),
("rs3803304", "C;C", Trait.longevity),
("rs3803304", "C;G", Trait.longevity),
("rs3803304", "G;G", Trait.longevity),
("rs6873545", "C;C", Trait.longevity),
("rs4590183", "C;C", Trait.longevity),
("rs1556516", "C;C", Trait.longevity),
("rs1556516", "C;G", Trait.longevity),
("rs1556516", "G;G", Trait.longevity),
("rs7137828", "C;C", Trait.longevity),
("rs7137828", "C;T", Trait.longevity),
("rs7137828", "T;T", Trait.longevity),
("rs1627804", "C;C", Trait.longevity),
("rs1627804", "A;A", Trait.longevity),
("rs1627804", "A;C", Trait.longevity),
("rs7844965", "A;G", Trait.longevity),
("rs7844965", "A;A", Trait.longevity),
("rs7844965", "G;G", Trait.longevity),
("rs61978928", "C;C", Trait.longevity),
("rs61978928", "C;T", Trait.longevity),
("rs61978928", "T;T", Trait.longevity),
("rs28926173", "C;C", Trait.longevity),
("rs28926173", "C;T", Trait.longevity),
("rs28926173", "T;T", Trait.longevity),
("rs146254978", "C;C", Trait.longevity),
("rs146254978", "C;T", Trait.longevity),
("rs146254978", "T;T", Trait.longevity),
("rs139137459", "A;G", Trait.longevity),
("rs139137459", "A;A", Trait.longevity),
("rs139137459", "G;G", Trait.longevity),
("rs3758391", "T;T", Trait.longevity),
("rs5882", "A;G", Trait.longevity),
("rs1042522", "C;G", Trait.longevity),
("rs333", ("46373456",), Trait.immunity),
("rs28379706", "T;T", Trait.intelligence),
("rs28379706", "C;T", Trait.intelligence),
("rs28379706", "C;C", Trait.intelligence),
("rs363039", "A;G", Trait.intelligence),
("rs4680", "A;A", Trait.intelligence),
("rs363039", "C;C", Trait.intelligence),
("rs1815739", "C;C", Trait.muscular_performance),
("rs1805086", "C;C", Trait.muscular_performance),
("rs1815739", "C;T", Trait.muscular_performance),
("rs1805086", "C;T", Trait.muscular_performance),
("rs1815739", "T;T", Trait.muscular_performance),
("rs4570625", "G;G", Trait.ocd),
("rs4565946", "C;C", Trait.ocd),
("rs1801131", "A;C", Trait.metabolism),
("rs1801131", "C;C", Trait.metabolism),
("rs1801133", "C;T", Trait.metabolism),
("rs1801133", "T;T", Trait.metabolism),
("rs2282679", "A;C", Trait.metabolism),
("rs2282679", "C;C", Trait.metabolism),
("rs12785878", "G;T", Trait.metabolism),
("rs12785878", "T;T", Trait.metabolism),
("rs1799945", "F;G", Trait.metabolism),
("rs4988235", "C;C", Trait.metabolism),
("rs182549", "C;C", Trait.metabolism),
("rs2187668", "A;A", Trait.metabolism),
("rs2187668", "A;G", Trait.metabolism),
("rs5030858", "T;T", Trait.metabolism),
("rs72921001", "C;C", Trait.metabolism),
("rs7903146", "T;T", Trait.metabolism),
("rs7903146", "C;C", Trait.metabolism),
("rs7903146", "C;T", Trait.metabolism),
("rs662799", "A;G", Trait.metabolism),
("rs662799", "G;G", Trait.metabolism),
("rs13119723", "A;A", Trait.metabolism),
("rs13119723", "A;G", Trait.metabolism),
("rs13119723", "G;G", Trait.metabolism),
("rs6822844", "G;G", Trait.metabolism),
("rs3184504", "C;T", Trait.metabolism),
("rs3184504", "T;T", Trait.metabolism),
("rs12913832", "A;A", Trait.eyes),
("rs12913832", "A;G", Trait.eyes),
("rs12913832", "G;G", Trait.eyes),
("rs28938473", "T;T", Trait.eyes),
("rs61753033", "T;T", Trait.eyes),
("rs61753034", "T;T", Trait.eyes),
("rs4778241", "A;A", Trait.eyes),
("rs4778241", "A;C", Trait.eyes),
("rs4778241", "C;C", Trait.eyes),
("rs7495174", "A;A", Trait.eyes),
("rs1129038", "A;A", Trait.eyes),
("rs1129038", "A;G", Trait.eyes),
("rs1129038", "G;G", Trait.eyes),
("rs916977", "A;A", Trait.eyes),
("rs916977", "A;G", Trait.eyes),
("rs916977", "G;G", Trait.eyes),
("rs1667394", "A;A", Trait.eyes),
("rs6152", "A;A", Trait.hair),
("rs6152", "A;G", Trait.hair),
("rs6152", "A;", Trait.hair),
("rs6152", "G;G", Trait.hair),
("rs1805009", "C;C", Trait.hair),
("rs1805009", "C;G", Trait.hair),
("rs1805007", "C;T", Trait.hair),
("rs1805007", "T;T", Trait.hair),
("rs1805008", "C;T", Trait.hair),
("rs1805008", "T;T", Trait.hair),
("rs1805006", "A;A", Trait.hair),
("rs1805006", "A;C", Trait.hair),
("rs11547464", "A;A", Trait.hair),
("rs11547464", "A;G", Trait.hair),
("rs35264875", "T;T", Trait.hair),
("rs7349332", "T;T", Trait.hair),
("rs11803731", "T;T", Trait.hair),
("rs17646946", "A;A", Trait.hair),
("rs1667394", "A;A", Trait.hair),
]
RSIDS = [Rsid(x[0], x[1], x[2]) for x in _RSIDS]
def parse_file(path: str) -> dict[str, str]:
"""parse a file into a dict that we can perform lookups with"""
with open(path) as genes:
return {x.split("\t")[0]: x for x in genes.readlines() if x.startswith("rs")}
def scan_genes(rsid_dict: dict[str, str]) -> list[Rsid]:
"""scan the given gene dictionary, returning a list of RSIDS that were detected"""
return [x for x in RSIDS if x.rsid in rsid_dict and x.detect(rsid_dict[x.rsid])]
if __name__ == "__main__":
filename = (
sys.argv[1]
if len(sys.argv) > 1
else input("Enter the location of the DNA data file: ")
)
rsid_dict = parse_file(filename)
rsids = scan_genes(rsid_dict)
for rsid in rsids:
print(rsid.info + "\n")