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 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
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