python; how to write output to text file

Question

With my code, I loop over files and count patterns in files. My code is as follows

from collections import defaultdict
import csv, os, re
from itertools import groupby
import glob


   def count_kmers(read, k):
        counts = defaultdict(list)
        num_kmers = len(read) - k + 1
        for i in range(num_kmers):
            kmer = read[i:i+k]
            if kmer not in counts:
                counts[kmer] = 0
            counts[kmer] += 1
        for item in counts:
            return(basename, sequence, item, counts[item])

    for fasta_file in glob.glob('*.fasta'):
        basename = os.path.splitext(os.path.basename(fasta_file))[0]
        with open(fasta_file) as f_fasta:
            for k, g in groupby(f_fasta, lambda x: x.startswith('>')):
                if k:
                    sequence = next(g).strip('>\n')
                else:
                    d1 = list(''.join(line.strip() for line in g))
                    d2 = ''.join(d1) 
                    complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A'}
                    reverse_complement = "".join(complement.get(base, base) for base in reversed(d1))
                    d3 = list(''.join(line.strip() for line in reverse_complement))
                    d4 = ''.join(d3)
                    d5 = (d2+d4)
                    counting = count_kmers(d5, 5)
                    with open('kmer.out', 'a') as text_file:
                        text_file.write(counting)

And my output looks like this

1035 1 GAGGA 2
1035 1 CGCAT 1
1035 1 TCCCG 1
1035 1 CTCAT 2
1035 1 CCTGG 2
1035 1 GTCCA 1
1035 1 CATGG 1
1035 1 TAGCC 2
1035 1 GCTGC 7
1035 1 TGCAT 1

The code works fine, but I cannot write my output to a file. I get the following error:

    TypeError                                 Traceback (most recent call last)
<ipython-input-190-89e3487da562> in <module>()
     37                 counting = count_kmers(d5, 5)
     38                 with open('kmer.out', 'w') as text_file:
---> 39                     text_file.write(counting)

TypeError: write() argument must be str, not tuple

What am I doing wrong and how can I solve this problem, to make sure that my code write the output to a txt file?

Answer 1

The original verions of count_kmers() did not contain a return statement, which means it has an implicit return None .

As you assign this to counting all of your errors became self explanatory.

After your edit, the end of the function looked like this:

for item in counts:
    return(basename, sequence, item, counts[item])

which returns a tuple with four values. It also exits the function on the first pass through the loop.