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?

You aren't returning anything from your functions, just printing things to the screen. Without an explicit return statement, a Python function returns None, which is what counting = count_kmers(d5, 5) will do, and when you try to ''".join(None) you will get that error — juanpa.arrivillaga
– juanpa.arrivillaga, Commented Sep 25, 2017 at 19:38
I changed my code (used return instead of print), but than I get the error that my write argument must be str and not tuple? — Gravel
– Gravel, Commented Sep 25, 2017 at 19:45

kdopen · Accepted Answer · 2017-09-25 19:52:07Z

4

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.

edited Sep 25, 2017 at 19:52

answered Sep 25, 2017 at 19:37

kdopen

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2 Comments

Gravel Over a year ago

I changed my code (used return instead of print), but than I get the error that my write argument must be str and not tuple?

kdopen Over a year ago

Because you are now returning a tuple - and you exit on the first pass of the loop

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