hash_sequence

A Rosetta Stone for getting hashsums

Contents

This is a repo to have examples on how to make hashsums for each language.

Functions:

• hash_sequence: convert a string into a reduced hash
• reduceMd5: transform an md5sum into a reduced hash

Usage

Python

with hash_sequence.py in your working dir

via import

import hash_sequence

# convert seqeunce to PN2.0 hash
seq  = "ACTG"
hash = hash_sequence.hash_sequence(seq)

# convert md5 hash to PN2.0 hash
md5 = 'f1f8f4bf413b16ad135722aa4591043e'
hash = hash_sequence.reduceMd5(md5, 56)

via command line

$ python hash_sequence.py -i ACGT
46054055969511637

$ python hash_sequence.py -m f1f8f4bf413b16ad135722aa4591043e
46054055969511637

$ python hash_sequence.py -l /path/to/inputs.txt
46054055969511637
85152937750931901
23743195715719382

Perl

use hash_sequence qw/hash_sequence/;

$seq  = "ACTG";
$hash = hash_sequence($seq);

Rust

see here for a Rust implementation with instructions.

FAQ

Can I transform a hash back to the string?

No, hashing is a one-way algorithm. There are brute-force methods such as hash2seq, but it is a computationally intensive method.

Are you worried about hash collisions with different alleles?

Formally this is possible but with md5sum itself, we have not observed collisions. See here for a small experiment: lskatz/mlst-hash-template#16.