I'm trying to count the frequency of SNPs every 100,000 base locations. I'm using a VCF file I've already prepared, and my professor showed me to use code such as below: inputfile=open("bcftools_snps.txt", 'r') X=0 for line in inputfile: A=line.split() if float(A[1]) < 100000: X=X+1 print("0-100000=", X) and thus far, I've done this with a new variable for 200,000-300,000 and so on and so forth. The issue is, there are 7 million placements, meaning I'd need to define 700 variables which just sounds horribly slow for one chromosome. Is there a more efficient way to do this? Continue reading...
