snp-counter

Counts all unique SNP mutations in a .map file

Prerequisites

A current installation of Python is required. For best results, please use Python 3.x and the latest PIP version.

For further information on how to install Python and update PIP, please go to the Python Download Page, and for installation help please go to the Python Installation Help Page

NOTE for Windows users: both PowerShell and Command Terminal require double quotes ("") around directories containing spaces.

NOTE for Linux, MacOS users: the Terminal requires double quotes ("") around directories containing spaces.

Instructions:

1. Copy snpCounter.py into any directory. If your terminal denies you access to other directories containing your .map files, copy snpCounter.py directly into the folder with the .map files.

2. Open a terminal in this directory, or change the directory of your terminal to the directory containing snpCounter.py

   ie. for Linux/MacOS:

   $ cd ~/Documents/"folder containing data"
   

   for Windows:

   cd "C:/Users/username/Documents/folder containing data/"
   

3. Run the following command:

   for Linux/MacOS

   python3 snpCounter.py <inputFile> <outputFile>
   

   for Windows

   snpCounter <inputFile> <outputFile>
   

   WARNING: the default output will overwrite any file in the directory named "output.csv" if no output file name is specified. Similarly, any existing file in the output directory with the same name as the output specified in the second argument will be overwritten.

   Alternatively, for Linux/MacOS, if you gain permission to execute snpCounter.py directly, you can run the program without needing to type "python3" before every terminal entry. This can be achieved by running the following command before first use:

   chmod +x snpCounter.py
   

   Subsequent usage can be now done as follows:

   ./snpCounter.py <inputFile> <outputFile>
   

Example

On Linux/MacOS:

if snpCounter.py is in the same folder as the data

 $ python3 snpCounter.py ecoliGenome.map mutations.csv

if snpCounter.py is in a different folder:

$ python3 snpCounter.py Documents/data/ecoliGenome.map mutations.csv

(both of the above two sample commands will write the output to "mutations.csv" inside the same folder as snpCounter.py)

Usage

Takes up to 2 input arguments, and requires valid .map file, generated from FASTA data, as first input argument.

Settings	Description
inputFile	Valid .map file generated from FASTA data.
outputFile	(OPTIONAL) Name of output file to be generated.

Help documentation (including usage and output information) can be accessed using the following command.

snpCounter.py help

Output

Output File	Description
filename	Count of position specific SNP mutations, in a comma separated plain text list. Default output is 'output.csv' and will be generated in same directory as snpCounter.py. Recommended output is .csv format

This program was written with Python 3.9.2 on Windows10 Pro Build 19041 and tested on both Windows10 Pro Build 19041 and Ubuntu 18.04.5 LTS