orig_seq_logo_demo.ipynb

Kernel: Unknown Kernel

# DNA Sequence Demonstration
# Author: Drishtii@
# Based on
# https://github.com/probml/pmtk3/blob/master/demos/seqlogoDemo.m

##!pip install -qq logomaker


import numpy as np

try:
    import pandas as pd
except ModuleNotFoundError:
    %pip install -qq pandas
    import pandas as pd
try:
    import probml_utils as pml
except ModuleNotFoundError:
    %pip install -qq git+https://github.com/probml/probml-utils.git
    import probml_utils as pml

try:
    import logomaker
except ModuleNotFoundError:
    %pip install -qq logomaker
    import logomaker
import matplotlib.pyplot as plt

li = [
    "atagccggtacggca",
    "ttagctgcaaccgca",
    "tcagccactagagca",
    "ataaccgcgaccgca",
    "ttagccgctaaggta",
    "taagcctcgtacgta",
    "ttagccgttacggcc",
    "atatccggtacagta",
    "atagcaggtaccgaa",
    "acatccgtgacggaa",
]

new_li = []
for i in range(len(li[0])):
    r = ""
    for j in range(len(li)):
        r += li[j][i]
    new_li.append(r)

position_weight_matrix = np.zeros((4, 15))
alphabets = ["a", "c", "g", "t"]
for seq in range(len(new_li)):
    for alphabet in range(len(alphabets)):
        position_weight_matrix[alphabet][seq] = new_li[seq].count(alphabets[alphabet]) / 5

df = pd.DataFrame(position_weight_matrix.T, columns=["A", "C", "G", "T"])
df.index = np.arange(1, len(df) + 1)

logos = logomaker.Logo(df)
logos.ax.set_xticks(np.arange(1, 16))
logos.ax.set_yticks(np.arange(3))
logos.ax.set_ylabel("Bits")
logos.ax.set_xlabel("Sequence Position")
pml.savefig("seqlogo.pdf")
plt.show()