Introduction

In class we worked on patterncount.py a module containing some functions for finding patterns in sequences, and prueba-bioinf.ipynb, a jupyter notebook testing some of the functions. In the notebook, we have two cells that have very similar code for reading files:

with open("vibrio-ori.txt") as f:
    Text = ""
    for line in f.readlines():
        line = line.strip()
        Text += line

Assignment

1. Convert the above fragment into a function that takes a filename as a parameter, and returns the contents as a single string.

2. Implement the FindClumps function described in Lesson 1.4 of the text. (The problem is also described in rosalind).

Upload your solutions in the course moodle.