file_rename.py

#!/usr/bin/env python3
# Peter L. Morrell - St. Paul, MN 17 October 2016

import os
import sys

"""A script to rename files, especially fastq files \
downloaded from the NCBI Sequence Read Archive."""

"""Known issues: 1) is only designed to work from the \
directory where files will be renamed and 2) will not \
except input files with a trailing newline!"""

Usage = """
file_rename.py - version 1
The script reads in a file containing a list of old and \
new files in the first and second column. It then checks \
for presence of a file by the same name in the current \
working directory. If the file is present (and the user \
has permissions) the file name is replaced with the name \
in the second column. Both old and new file names listed \
should be unique. The list of file names can have a header \
after a comment "#" symbol.

Usage:
    file_rename.py [file_list.txt]
"""

#   Expects a filename as the only argument
if not sys.argv[1:]:
    print(Usage)
    exit(1)

#   Create a dictionary that will hold old and new file names
file_data = {}
#   Read the file in line-by-line
try:
    with open(sys.argv[1]) as f:
        for line in f:
            #   Skip the header lines
            if line.startswith('#'):
                continue
            #   Split the two columns, then write to key & value
            else:
                names = line.strip().split()
                file_data[names[0]] = names[1]
except IOError as ex:
    print("File open issue: " + ex.strerror)

#    Get the path to the current directory
cwd = os.getcwd()
files = []
#    List the files in the current directory
files = os.listdir(cwd)

#    Create a new dictionary with only the files in our list that \
#    match file names in the current direcoty
re_names = {k: file_data[k] for k in files if k in file_data}

#    Use keys and values to replace old file names with new
for i, j in re_names.items():
    os.rename(i, re_names[i])