Thursday, May 1, 2014

Checking md5 sums for lots of files from Windows

I run a lot of local BLAST searches on Windows machines. When you download a blast database from NCBI, you should also download the md5 file so you can check that the downloaded file is exactly the same as the one on the server (sometimes there can be fidelity issues when transferring data). Linux has a handy tool for comparing md5 sums, called md5sum. Example.

For Windows, there isn't a built in md5sum tool, so you've got to be a little more creative (or you could just use HashCheck, but let's be adventurous). I wrote a python script that will do it (it will also run on Linux, but that seems kind of pointless given the built-in option):

Call the script from the same directory as all of the .md5 files and datafiles (if you don't want to check every .md5 file, just change the md5_glob variable.
import os
from glob import iglob
import hashlib
#assumes that the directory contains text files with md5 sums named *.md5
#and that the first line of those files contain an md5 hash, followed by
#whitespace followed by the name of another file
#the other file should also be in the directory

md5_glob = '*.md5'

def md5_for_file(f, block_size=2**22):
#source:, the answer from Lars Wirzenius
    md5 = hashlib.md5()
    while True:
        data =
        if not data:
    return md5.hexdigest() #changed from example

def read_md5_from_file(filename):
    #reads file filename, and
    with open(filename) as infile:
        (hash, name) = infile.readline().split()
    return (hash, name)

total_comparisons = 0
good_comparisons = 0
for md5_file_name in iglob(md5_glob):
    (reference_hash, data_file_name) = read_md5_from_file(md5_file_name)
        data_file = open(data_file_name, 'rb')
        print('Warning: cannot open file ' + data_file_name)
        data_file = None
    if data_file is not None:
        total_comparisons += 1
        data_file_hash = md5_for_file(data_file)
        if data_file_hash == reference_hash:
            good_comparisons += 1
            print("hashes don't match for file " + data_file_name)
print("Total files examined: " + str(total_comparisons))
print("Files with good md5 sum: " + str(good_comparisons))

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