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Python class which reads and interprets 23andMe raw genotype data.
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GenoMe.py
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README.md

README.md

GenoMe: interpret your 23andMe data

GenoMe is a Python module which reads and interprets 23andMe raw genotype data. It Support simple wellness report from 23andMe, and searching your genotype with related traits at SNPedia.

Quick-look

>>> from GenoMe import Geno
>>> g = Geno("/path/to/your/raw/data.txt")
  • Geno.report_wellness() prints out wellness report provided by 23andMe API.
>>> g.report_wellness()
=============================== WELLNESS REPORT =============================== 

< Alcohol Flush Reaction >
--------------------------------------------------------------------------------
The marker we tested comes in two different forms, the G variant and the A varia
nt. The A variant results in an enzyme that is less efficient at breaking down a
cetaldehyde. The A variant is also known as c.1510G>A, Glu487Lys, and Glu504Lys.
 This marker has been studied the most in people of East Asian descent.

  rsID: rs671
  Yours: G;G - homozygous
  Detail: 2 | Alcohol Flush: Normal, doesn't flush. Normal hangovers. Normal ris
k of Alcoholism. Normal risk of Esophageal Cancer. Disulfiram is effective for a
lcoholism. | 60.2% of JPT

...
  • Geno.type_id(rsid) prints out specific SNP of input rsid and its related trait written in SNPedia.
>>> g.type_id("rs28897696")
rs28897696 | G;G | 0 | normal | 0.0% of JPT
rsid chr pos genotype
492260 rs28897696 17 38469446 GG
  • Geno.type_trait(trait) prints out all SNPs related to input trait, written in SNPedia.
>>> g.type_trait("baldness")
rs6152 | G;G | 0.5 | able to go bald | 100.0% of JPT
rs2223841 | T;T | 1.2 | more likely to go bald before age 40 | 100.0% of JPT
rs6152 | G;G | 0.5 | able to go bald | 100.0% of JPT
rs2223841 | T;T | 1.2 | more likely to go bald before age 40 | 100.0% of JPT
rs2180439 | C;T | 2.5 | Increased risk of Male Pattern Baldness. | 44.2% of JPT
rs11683401 | C;T |  | --% of JPT
rs2073963 | G;G | 2.5 | increased risk of baldness | 18.6% of JPT
rs1511061 | T;T |  | --% of JPT
 * more details at https://www.snpedia.com/index.php/baldness

Reference Population

You can also change the population used to report genotype ratio, other than 'JPT'. report_wellness, type_id, and type_trait supports ref_population option to input population code.

>>> g.report_wellness(ref_population="CEU")
>>> g.type_id("rs28897696", ref_population="CHB")
>>> g.type_trait("baldness", ref_population="ASW")

For more information about populations and their code, see this page.

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