mutation-rate-intervals

This software calculates a confidence interval for the mutation rate from a set of observed containment indices under a simple nucleotide mutation process. In this model, a sequence B evolves from a sequence A by independently mutating every nucleotide with probability p. We then observe the scaled containment indices as a result of the mutation process. The software then generates a confidence interval for the mutation rate p.

Install (requires conda or mamba)

We recommend installation within an isolated conda environment. You can create a conda environment with all dependencies installed like so:

1. git clone this repo and cd in:

git clone https://github.com/KoslickiLab/mutation-rate-ci-calculator
cd mutation-rate-ci-calculator

2. Use conda or mamba to create the mrcc environment with all dependencies installed:

conda env create --file environment.yml

If you have mamba installed, feel free to use it here to speed things up. If you haven't installed conda or mamba, install it first via Miniforge or Miniconda.

3. Activate the virtual environment and install this software with pip:

conda activate mrcc
pip install -e '.'

You should now be able to run the help for p_from_scaled_containment:

python -m mrcc.p_from_scaled_containment --help

Quick start

To compute a p confidence interval from an observed number of scaled containment indices:

python -m mrcc.p_from_scaled_containment -L 100K -k 21 -c 0.95 --sccon 0.10605
L       k       conf    Cks     CLow    CHigh   pLow    pHigh
100000  21      0.95    0.10605 0.10046 0.11191 0.09623 0.10655

Output

In the example above, the L, k, conf, and Cks values are the input number of k-mers, k-mer size, desired confidence level, and observed scaled MinHash value respectively. The CLow and CHigh give the left and right 95% confidence interval around the true containment value. The pLow and pHigh give a confidence interval that is at least as wide as the 95% confidence interval around the true mutation rate p. Note that average nucleotide identity (ANI) is equal to 1-p.

How to choose L and other parameters

In reality, you may not know L. In such cases, we recommend that you estimate it from what you know. For example, if what you know is that the number of distinct (i.e. counting duplicates only once) k-mers in A is nA and in B is nB, then you can set L = (nA + nB) / 2. You can also try setting L = min(nA, nB) or L = max(nA, nB).

You may also want to get a confidence interval on p from the number of mutated k-mers N, but you might only known the number of shared k-mers, i.e. the number of k-mers in both A and B. If this number is n, then you can set N = L - n.

Note that the programs consider L (uppercase) as the number of kmers in the sequence, and l (lowercase) as the number of nucleotides, with l = L + k-1.

Prerequisites

• python3
• scipy
• numpy

For computing confidence intervals, only scipy is required. An optional module, mpmath, will be used if present (as described below).

Numpy is only used by the simulation programs.

Two addition packages are used if present: mpmath and mmh3.

mpmath is a multi-precision package, used here to avoid numerical problems that can occur for very low mutation probabilities (e.g. 1e-8). If the module is not present standard python floating-point is used instead.

mmh3 is a wrapper for MurmurHash3, used here for hashing kmers for bottom sketches. If the module is not present the hashing options in simulate_nucleotide_errors are not available.

Usage Details

python -m mrcc.p-from-scaled-containment.py

Compute confidence interval for the mutation rate p, given the observed number of mutated k-mers

optional arguments:
  -h, --help            show this help message and exit
  --sccon SCCON [SCCON ...]
                        observed MinHash Containment (input one or more values, separated by a space)
  --length LENGTH       number of nucleotides in the sequence
  -L NUM_UNIQUE_KMERS, --num-unique-kmers NUM_UNIQUE_KMERS
                        number of unique k-mers in the sequence
  --scaled SCALED       scaling factor of the sketch
  -k KSIZE, --ksize KSIZE
                        kmer size
  -c CONFIDENCE, --confidence CONFIDENCE
                        size of confidence interval, (value between 0 and 1)
  -s SEED, --seed SEED  random seed for simulations
  --debug               debug
  --debug_options [{nocache,nojmonotonicity,nsanity} [{nocache,nojmonotonicity,nsanity} ...]]
                        Specify one or more debugging options, separated by a space