fq_to_fa.py

# this works on art_illumina fq output file
# I needed to convert them to fa to run the superbubble performance tool
import sys
import os

if len(sys.argv) != 3:
    print("Please give two arguments [input_file_name] [output_file_name]")
    
fastq_f = open(sys.argv[1], "r")
lines = fastq_f.readlines()

fasta_output = []
for idx, l in enumerate(lines):
    if l.startswith("@"):
        l = ">" + l
        fasta_output.append(l)
        fasta_output.append(lines[idx+1])


output_f_name = str(sys.argv[2])
fasta_f = open(output_f_name, "w")
for l in fasta_output:
    fasta_f.write(l)