presig: Transform a MAF file into the inputs of signet / sparsesigs
Eric T Dawson
Nov 2019
Introduction
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 <MAF> -f <FASTA>
This will generate two files (<MAF>.SBS96.tsv and <MAF>.ID83.tsv) in the current directory.
Convert a MAF file to the SigProfiler simple text format
python presig/presig.py -m <MAF> -f <FASTA> -s -u > <outputfile>.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 <MAF>.SBS96.tsv
Questions and bug reports
Please post an issue on the GitHub if you have a question or find a bug.