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https://github.com/edawson/presig
Convert MAF files to formats used as input to mutational signature programs including SigProfiler
https://github.com/edawson/presig
Last synced: about 2 months ago
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Convert MAF files to formats used as input to mutational signature programs including SigProfiler
- Host: GitHub
- URL: https://github.com/edawson/presig
- Owner: edawson
- License: mit
- Created: 2019-11-04T20:44:18.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2024-02-08T02:01:15.000Z (11 months ago)
- Last Synced: 2024-02-08T03:21:04.374Z (11 months ago)
- Language: Python
- Homepage:
- Size: 357 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
presig: Transform a MAF file into the inputs of signet / sparsesigs
---------------------------------------
Eric T Dawson
Nov 2019
## Introduction
[presig](https://github.com/edawson/presig) generates count matrices of single-base (SBS) and
indel (ID) features for input to SigProfiler, SignatureAnalyzer, and signet/sparsesigs. It takes a
MAF file as input, as well as a corresponding references FASTA file.
## Requirements
presig requires pyfaidx for parsing FASTA files and pycotap for testing.
## Installation
```
git clone --recursive https://github.com/edawson/presig
cd presig/
pip install -r requirements.txt -e .
```
## Basic usage
presig is primarily designed to be used at the command line,
though you can also import its individual functions
into a python environment if desired.
### Convert a MAF file to feature counts
```
python presig/presig.py -m -f
```
This will generate two files (`.SBS96.tsv` and `.ID83.tsv`) in the current directory.
### Convert a MAF file to the SigProfiler simple text format
```
python presig/presig.py -m -f -s -u > .txt
```
### Run SigProfiler (including installing SigProfilerHelper)
To run SBS96 signatures using the TSV counts matrix generated using presig:
```
git clone --recursive https://github.com/edawson/sigprofilerhelper
python sigprofilerhelper/run_sigprofiler.py -c 16 -i 1000 -s 1 -e 7 -t .SBS96.tsv
```
## Questions and bug reports
Please post an issue on the [GitHub](https://github.com/edawson/presig) if you have a question or find a bug.