per_base_quality.py

from Bio import SeqIO
import seaborn as sns
from collections import defaultdict
import gzip
import sys

q_per_base = defaultdict(list)
for record in SeqIO.parse(gzip.open(sys.argv[1], 'rt'), "fastq"):
    for n, q in zip(record.seq, record.letter_annotations["phred_quality"]):
        q_per_base[n].append(q)
        
ax = sns.violinplot(data=list(q_per_base.values()))
ax.set_xticklabels(list(q_per_base.keys()))
fig = ax.get_figure()
fig.savefig(fname="Per_base_quality.png")