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:

1. Let’s start with the usual imports:

   from collections import defaultdict
   import gzip
   import numpy as np
   import matplotlib.pylab as plt

2. 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)

3. 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):
      ...