Question

I’m writing a python script to replace strings from a each text file in a directory with a specific extension (.seq). The strings replaced should only be from the second line of each file, and the output is a new subdirectory (call it clean) with the same file names as the original files, but with a *.clean suffix. The output file contains exactly the same text as the original, but with the strings replaced. I need to replace all these strings: ‘K’,’Y’,’W’,’M’,’R’,’S’ with ‘N’.

This is what I’ve come up with after googling. It’s very messy (2nd week of programming), and it stops at copying the files into the clean directory without replacing anything. I’d really appreciate any help.

Thanks before!

import os, shutil

os.mkdir('clean')

for file in os.listdir(os.getcwd()):
    if file.find('.seq') != -1:
        shutil.copy(file, 'clean')

os.chdir('clean')

for subdir, dirs, files in os.walk(os.getcwd()):
    for file in files:
        f = open(file, 'r')
        for line in f.read():
            if line.__contains__('>'): #indicator for the first line. the first line always starts with '>'. It's a FASTA file, if you've worked with dna/protein before.
                pass
            else:
                line.replace('M', 'N')
                line.replace('K', 'N')
                line.replace('Y', 'N')
                line.replace('W', 'N')
                line.replace('R', 'N')
                line.replace('S', 'N')

Answer 1

some notes:

1. string.replace and re.sub are not in-place so you should be assigning the return value back to your variable.
2. glob.glob is better for finding files in a directory matching a defined pattern…
3. maybe you should be checking if the directory already exists before creating it (I just assumed this, this could not be your desired behavior)
4. the with statement takes care of closing the file in a safe way. if you don’t want to use it you have to use try finally.
5. in your example you where forgetting to put the sufix *.clean 😉
6. you where not actually writing the files, you could do it like i did in my example or use fileinput module (which until today i did not know)

here’s my example:

import re
import os
import glob

source_dir=os.getcwd()
target_dir="clean"
source_files = [fname for fname in glob.glob(os.path.join(source_dir,"*.seq"))]

# check if target directory exists... if not, create it.
if not os.path.exists(target_dir):
    os.makedirs(target_dir)

for source_file in source_files:
   target_file = os.path.join(target_dir,os.path.basename(source_file)+".clean")
   with open(source_file,'r') as sfile:
      with open(target_file,'w') as tfile:
         lines = sfile.readlines()
         # do the replacement in the second line.
         # (remember that arrays are zero indexed)
         lines[1]=re.sub("K|Y|W|M|R|S",'N',lines[1])
         tfile.writelines(lines)

print "DONE"

hope it helps.