https://github.com/edawson/assisi
A somatic mutation signature simulator
https://github.com/edawson/assisi
autoencoders mutational-signatures simulation snvs
Last synced: 3 months ago
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A somatic mutation signature simulator
- Host: GitHub
- URL: https://github.com/edawson/assisi
- Owner: edawson
- Created: 2017-09-27T22:24:28.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2020-02-13T18:12:36.000Z (over 5 years ago)
- Last Synced: 2025-01-07T20:47:19.899Z (4 months ago)
- Topics: autoencoders, mutational-signatures, simulation, snvs
- Language: Python
- Size: 86.9 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
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README
assisi: another somatic signature simulator
-------------------------------------------
Eric T. Dawson
September 27 2017
## What is it?
`assisi` is a python package that simulates mutational signature profiles (i.e. counts / proportions of trinucleotide context mutations) using Monte Carlo simulation.
## Required / useful files
We've included the cosmic mutational signatures probabilities from deconstructSigs (https://github.com/raerose01/deconstructSigs).
## Running assisi
`python assisi.py -h` for help.
## Typical usage:
The following command will generate a single mutational catalog with 1000 total mutations.
`-r` specifies that assisi should generate a random number of signatures (1-10) and assign
random proportions to each of those ten signatures. The sum of the proportions is 1.0,
with some error.
`-i` is the COSMIC SBS96 mutational context probabilities; each row is a signature, and each column
is the proportion of that mutational context in the signature.
```
python assisi.py -i cosmic_file.tsv -n 1000 -r > catalog.tsv
```
Rules for COSMIC sig files:
No headers
Tab separated
No restriction on number of rows
There must be 96 columns (for now)
The next version of assisi will use a tidy format for this data.
The output of assisi when run as above is a single line with the following columns:
```
...
```
Multiple catalogs can be generated by passing the `-m` flag and a desired number of catalogs:
```
## Simulate 1000 catalogs
python assisi.py -i cosmic_file.tsv -n 1000 -r -m 1000 > catalogs.tsv
```
Assisi uses the Python multiprocessing package to optionally generate catalogs in parallel.
We recommend using this feature when simulating more than one catalog, as it decreases runtime
proportional to the number of available compute cores and does not affect results in any way.
```
## Simulate 1000 catalogs, with 4 threads
python assisi.py -i cosmic_file.tsv -n 1000 -r -m 1000 -t 4 > catalogs.tsv
```
## Installation
`assisi` is written in barebones python3 and is backwards-compatible with python 2.7 - no installation necessary.