[FIXED] Concatenating fasta files in folder into single file in python

Issue

I have multiple fasta sequence files stored in a folder within my current working directory (called "Sequences") and am trying to combine all the sequences into a single file to run a MUSLCE multiple sequence alignment on.

This is what I have so far and it is functional up until the output_fas.close(), where i get the error message FileNotFoundError: [Errno 2] No such file or directory: './Sequences'

Here is the code:

 import os
os.getcwd() #current directory
DIR = input("\nInput folder path containing FASTA files to combine into one FASTA file: ")
os.chdir(DIR)
FILE_NAME = input("\nWhat would you like to name your output file (e.g. combo.fas)? Note: "
                  "Please add the .fas extension: ")
output_fas = open(FILE_NAME, 'w')
file_count = 0

for f in os.listdir(DIR):
    if f.endswith(( ".fasta")):
        file_count += 1
        fh = open(os.path.join(DIR, f))
        for line in fh:
            output_fas.write(line)
        fh.close()

output_fas.close()
print(str(file_count) + " FASTA files were merged into one file, which can be found here: " + DIR)

When i input the directory i input it as './Sequences' which successfully changes the directory.

Not quite sure what to do. I adjusted the code before and it successfully created the new files with all the sequences concatenated together, however it ran continuously and would not end and had multiple repeats of each sequence.

Appreciate the help!

Solution

The error should occur before the output_fas.close(), and should be seen at the os.listdir(DIR) call. The problem is that DIR becomes meaningless as soon as you execute the os.chdir(DIR) command. DIR was provided as a relative path, and os.chdir(DIR) changes to the new directory, making the old relative path no longer correct relative to the new directory.

If you're going to use os.chdir(DIR), then never use DIR again, and just change your loop to:

# Use with statement for guaranteed deterministic close at end of block & to avoid need
# for explicit close
with open(FILE_NAME, 'w') as output_fas:
    file_count = 0
    for f in os.listdir():  # Remove DIR to list current directory
        if f.endswith(".fasta"):
            file_count += 1
            # Use a with for same reason as above
            with open(f) as fh: # Don't join to DIR because f is already correctly in current directory
                output_fas.writelines(fh)  # writelines does the loop of write calls for you

Answered By - ShadowRanger