I want to add to an array as I would a list from a for loop but to do so I need to create an empty array first and add to it. Every suggestion I've seen on this site makes it so the old array is overwritten by a new array which seems incredibly silly. The file I am pulling form is 150 x 180,000 data points so lists won't cut it. It seems insane that creating an empty array is some impossible task if making a list is so simple. This is my code for now but I want to cut the list out of the equation from Bio import SeqIO from Bio.SeqUtils import gc_fraction import matplotlib.pyplot as plt import gzip import numpy as np with gzip.open("data.fastq.gz",'rt') as input_file: sio = SeqIO.parse(input_file, "fastq") numdata = [] for r in sio: numdata.append(r.letter_annotations['phred_quality']) npa = np.array(numdata) plt.boxplot(npa,showfliers = False) plt.title("Quality Score Boxplot") plt.xlabel("Number of Basepairs") plt.ylabel("Number of Reads") plt.show() Continue reading...
