SNV-FEAST 0.0.8

A package to get signature SNVs from a given strain and set of sink and sources, using MIDAS output

SNV-FEAST

SNV-FEAST is a method to generate signature SNVs for input into FEAST (Shenhav et al. 2019) from MIDAS (Nayfach et al. 2017) SNV output.

Quick start tutorial

1. Install SNV-FEAST with pip

python3 -m pip install SNV-FEAST==0.0.4

Option 1: Run as a python module in your code

1. Install SNV-FEAST with pip
2. Set up your directories and config
3. use the module

from snv_feast import snv_feast
snv_feast.signature_snvs("Bacteroides_uniformis_57318", 5, 1, 200, "<directory to your config file>config.yaml")

Option 2: Run as a command line tool

1. git clone this repository
2. Set up your directories and config
3. Run CLI script

python snv_feast_cli.py --strain Bacteroides_uniformis_57318 --min_reads 5 --start_index 1 --end_index 200 --config_file_path <directory in which you cloned this repo>/snv-feast/configs/config.yaml

##Setting up directory and config file 'example_template' shows how the directory and config should be set up

Required input:

1. midas_output: MIDAS output with a subdirectory called 'snps/' with it's own subdirectory for each species. In side each species subsubdirectory are two bzipped files 'snps_depth.txt.bz2' and 'snps_ref_freq.txt.bz2'
2. sink_source.csv : a comma-delimited file with the sink source configuration. It should have the accession numbers in the first column for each sink of interest, and in the following columns, the accession numbers for the sources for each sink

Try running with 'example_1' on command line

Run in terminal:

snv_feast_cli --strain Bacteroides_uniformis_57318 --min_reads 5 --start_index 1 --end_index 200 --config_file_path /Users/leahbriscoe/Documents/FEASTX/snv-feast/configs/config.yaml

Try running with 'example_1' in a python script

import snv_feast
snv_feast.signature_snvs(strain="Bacteroides_uniformis_57318", min_reads=5, start_index=1, end_index=200, config_file_path="/Users/leahbriscoe/Documents/FEASTX/snv-feast/configs/config.yaml")