Your mission for today is to write a script that checks a 23 and Me genotype file for several groups of SNPs that are associated with blue eyes. The SNPs in question are in the file “blueeyepanel.txt” in the Dropbox. The format of the file is “genotype, SNP, haplotype block”. Genotype is the derived genotype common in people with the blue eye variant discussed in the last post. SNP is the SNP identifier. Haplotype block is the code name for…
In this week’s exercise, we’re going to practice loops and lists in Python by looping through a 23 and me file to pull out data that matches a list of SNPs of interest. Before we get into the coding, I think it’s worth exploring how we arrive at such a list. In order to write a useful program, you need to understand the problem it’s solving. The raw information As I mentioned previously, I have access to my own 23 and…
Last week, you made a script that takes a “panel” of SNPs where a particular variant allele is associated with blue eyes in Europeans, parses an individual’s 23 and Me results to check their SNP status for each site in the panel, and reports back to the user. This week, I want you to modify your “Genome Horoscope”project with a couple of goals in mind: Define functions that do distinct parts of the script’s work. Make the script a little…
I just happen to have a file with 960,628 lines of personal SNP data from 23 and Me burning a hole in my hard drive. I’m one of the lucky people who gets 23 and Me’s extended health information because I bought my genotype at the right time, before the FDA got all handsy. But if I wanted to do more with that information on my own, could I? If I wanted to search for SNPs and traits one by…