Hello

I am trying to find specific sequences sequences from a FASTA file and write them to a text file In a 'sliding window' fashion using biopython.

This is what I have so far:

from Bio import SeqIO

input_file = open('sequences.fasta', 'r')
output_file = open('output.fasta', 'a')

def chunks(seq, win, step):
    seqlen = len(seq)
    for i in range(0,seqlen,step):
        j = seqlen if i+win>seqlen else i+win
        yield seq[i:j]
        if j==seqlen: break

for gene in SeqIO.parse(input_file, "fasta"):
    seq = gene.seq
    for subseq in chunks(seq,150,1):
        if 'desired sequence' in gene.description:
            print(gene.description)
            print(subseq)

output_file.close()
input_file.close()

This seems to work fine using the 'print' command but my code fails when I try to write to a file by replacing the 'print' commands for:

        SeqIO.write(gene.description, output_file, "fasta")
        SeqIO.write(subseq, output_file, "fasta")

I am new to coding/python and would appreciate if anyone could help me out with this.

Thanks