looselab/readfish-tools

Utility command line tools for helping run readfish

readfish-tools

readfish-tools is a suite of command line utilities to ease the set up and analysis of readFish experiments.

Installation

pip install rf_tools

or

git clone https://github.com/LooseLab/rf_tools
cd rf_tools
python3 -m venv venv
source venv/bin/activate
pip install -U pip setuptools wheel
pip install -e .

Usage

usage: rf_tools [-h] {setup,update} ...

rf_tools suite

optional arguments:
  -h, --help      show this help message and exit

subcommands:
  {setup,update}  additional help
    setup         create a simple barcode based deplete/enrich experiment TOML.
    update        Update an existing simple toml file by removing or adding barcodes.

##Subcommands ###Setup - Interactively create a TOML file for running a read fish barcoding experiment.

usage: rf_tools setup [-h] --toml TOML [--no-minknow] [--mk-host MK_HOST] [--mk-port MK_PORT] [--use_tls]
                  [--adventure]

optional arguments:
  -h, --help         show this help message and exit
  --toml TOML        Path to the TOML file.
  --no-minknow       Do not attempt to use the minknow API, default False.
  --mk-host MK_HOST  Address for connecting to MinKNOW, default localhost.
  --mk-port MK_PORT  Port for connecting to MinKNOW, default 9501.
  --use_tls          Use TLS for connecting to MinKNOW, default False.
  --adventure        How about a little light role play?

The toml argument is required, as this is the path to write the toml file to. An example command would be:

rf_tools setup --toml example_test.toml

###Update - Interactively update an existing toml file to create a .toml_live file, to update a readfish barcoding experiment mid run.

usage: rf_tools update [-h] --toml TOML

optional arguments:
  -h, --help   show this help message and exit
  --toml TOML

Toml argument is required, as this is the TOML file to update. An example command would be

rf_tools update --toml example_test.toml