Finding genomic features from sequencing annotations
We will conclude this chapter and this book with a simple recipe that suggests that sometimes you can learn important things from simple unexpected results, and that apparent quality issues might mask important biological questions.
We will plot read depth – DP – across chromosome arm 2L for all the parents on our crosses. The recipe can be found in Chapter04/2L.py.
How to do it…
We’ll get started with the following steps:
- Let’s start with the usual imports:
from collections import defaultdict import gzip import numpy as np import matplotlib.pylab as plt
- Let’s load the data that we saved in the first recipe:
num_parents = 8 dp_2L = np.load(gzip.open('DP_2L.npy.gz', 'rb')) print(dp_2L.shape) - And let’s print the median DP for the whole chromosome arm, and a part of it in the middle for all parents:
for i in range(num_parents): ...