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