README.md

MITOMI Analysis Package

This Python package condenses the MITOMI initial analysis scripts into a simple suite of command line tools. The package is dependent on Python3, which you can grab with Homebrew:

$ brew install python3

Installation

Installation is as simple as cloning this repository and running the setup.py file as below:

$ git clone https://github.com/FordyceLab/mitomi_analysis.git
$ cd mitomi_analysis
$ python3 setup.py install

If installation is successful, you should now have the mitomi command line tool. You can check if this is that case by using the which command:

$ which mitomi

This command should return /usr/local/bin/mitomi. If nothing is returned, your installation was unsuccessful.

After installation, you can optionally remove the repository, as it is no longer needed:

$ cd ..
$ rm mitomi_analysis

Usage

The mitomi tool has six basic subcommands. These commands include:

• concat - concatenate .gpr files from different channels when imaging a device (replaces gprFilesToConcatFile.py)
• chip-analysis - outputs many plots that can be used to diagnose issues with the MITOMI run and check for consistency (replaces chipAnalysis.py)
• process - processes the raw concatenated files to calculate intensity ratios and other metrics (replaces processConcat_PR8.py)
• scatter-plot - create scatter plots to compare the two replicates within a device (replaces scatterPlotRep1vsRep2.py)
• prereduce - prepare files for running fREDUCE (replaces outputDataForfREDUCE_newConcatFiles.py)
• reduce - runs fREDUCE (replaces runMultiFREDUCE.py)

Each subcommand has a help string that can be summoned using the -h flag, for example $ mitomi concat -h. These help strings specify the inputs necessary to run each subcommand.

Note: *the reduce subcommand has not yet been tested since fREDUCE cannot be compiled on my 64-bit machine