Quality of sequence reads

This script plots the sequencing quality scores from an FASTQ file along with the sequence (base calls).

# Code source: Patrick Kunzmann
# License: BSD 3 clause

from io import StringIO
import matplotlib.pyplot as plt
import numpy as np
import biotite
import biotite.sequence.io.fastq as fastq

# Sample FASTQ file from https://en.wikipedia.org/wiki/FASTQ_format
fastq_content = StringIO("""
@SEQ_ID
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
""")


fastq_file = fastq.FastqFile.read(fastq_content, offset="Sanger")
sequence, scores = fastq.get_sequence(fastq_file, "SEQ_ID")
figure, ax = plt.subplots(figsize=(8.0, 2.0))
ax.bar(
    x=np.arange(len(sequence)),
    height=scores,
    color=biotite.colors["orange"],
    width=1.0,
    linewidth=1,
    edgecolor="white",
)
# -1 to put space between Y-axis and sequence
ax.set_xlim(-1, len(sequence))
# The range of Phred scores
ax.set_ylim(0, 40)
ax.set_ylabel("Phred score")
ax.spines["right"].set_visible(False)
ax.spines["top"].set_visible(False)
ax.spines["bottom"].set_visible(False)
# Show sequence as X-axis ticks
ax.set_xticks(np.arange(len(sequence)))
ax.set_xticklabels(sequence.symbols)
ax.xaxis.set_ticks_position("none")
figure.tight_layout()
plt.show()