Extract all entries from a FASTQ file with names not present in a FASTA file

fastq-to-fasta.py

from Bio.SeqIO.QualityIO import FastqGeneralIterator

corrected_fn   = "my_input_fasta.fas"
uncorrected_fn = "my_input_fastq.ftq"
output_fn      = "differences_fastq.ftq"

corrected_names = set() # Use a set instead of a list
for line in open(corrected_fn):
        if line[0] == ">":
                read_name = line.split()[0][1:] 
                corrected_names.add(read_name) # Add value to set

# corrected_names.sort() # No need, a set is orderless and optimized for search

handle = open(output_fn, "w")
for title, seq, qual in FastqGeneralIterator(open(input_fastq_fn)) :
        if title not in corrected_names:
                handle.write("@%s\n%s\n+\n%s\n" % (title, seq, qual))
handle.close()