aabiddanda

*.png
*.pdf

aabiddanda

[flake8]
max-line-length = 120
exclude=
  .git,
  .github,
  env,
  venv,
  build,
  dist
ignore=

aabiddanda

Interpolating genetic maps

In order to run this script you would need to run:

python3 interp_genmap.py --snp test.snp --genmap test_chr20_22.txt --morgans True

the module requirements for this are:

aabiddanda

"""
GANTT Chart with Matplotlib
Sukhbinder
Inspired from
https://sukhbinder.wordpress.com/2016/05/10/quick-gantt-chart-with-matplotlib/
"""
import datetime as dt
import matplotlib.pyplot as plt
import matplotlib.font_manager as font_manager
import matplotlib.dates

aabiddanda

#!/usr/local/bin/python3

'''
	Outputting audio representation of the 
		geography of a genetic variant (from 1000 Genomes)
'''

import argparse as arg
import subprocess as sp
import requests as req

aabiddanda

  # Function to convert R matrices to LaTeX 
  mat2tex <- function(mat, mat.name=NA){
    mat.string <- "\\setcounter{MaxMatrixCols}{15}$$\n"
    if (!is.na(mat.name)) {
      mat.string <- paste(mat.string, mat.name, "=") 
    }
    mat.string <- paste(mat.string, "\\begin{bmatrix} \n")
    n <- dim(mat)[1]
    m <- dim(mat)[2]

aabiddanda

	#Usage : <file> <column>
	mawk_stats(){
		file=$1
		col=$2
		mawk -v c=$col '{if(min==""){min=max=$c}; 
			if($c > max){max=$c}; if($c < min){min=$c}; sum+=$c; n+=1}
			END {printf "Min\tMax\tMean\tN\n%.3f\t%.3f\t%.3f\t%.0f\n",min, max ,sum/n, n}' $file
	}