gstripe 1.0.0

Graph-based stripe caller using chromain interaction data.

gStripe

Graph-based architectural stripe caller.

Requirements:

• Python >= 3.10
• Operating system: Linux (Ubuntu 20.04 or higher, recommended) or Windows 10 (or higher).
• All the dependencies listed in pyproject.toml, notably numpy >= 2.0.0 and igraph >= 0.11.5.

Installation

1. Optional, but recommended: Create and activate a python envrionment using pyenv, Conda or Mamba.
2. Install gStripe, depending on the chosen source:
   • Install from PyPI (recommended): pip3 install gstripe
   • Installing directly from github: run pip install git+https://github.com/SFGLab/gStripe.git.

To verify, that the installation proceeded correctly, you can do the following:

1. Run python -m gstripe.gstripe --help: you should see the help message. If not, check if the correct environment has been activated.
2. Run gStripe on an example file provided in examples/basic_test.bedpe in the github repository or in the .zip archive, using the following command: python -m gstripe.gstripe basic_test.bedpe .. The console output should end with [INFO] main(0.06s): All done. (timing may vary) and two new files should be created: ./basic_test.bedpe.gstripes_raw.tsv (results) and basic_test.bedpe.gstripe.log (log).

Usage

The gStripe architectural stripe caller uses a discrete set of interactions (such as chromatin loops) to perform calling.

Run python -m gstripe.gstripe input_interactions_file.bedpe output_directory to call the stripes using interactions from input_interactions_file.bedpe and place the results (input_loops_file.bedpe.gstripes_raw.tsv by default) and the log file in output_directory. This results in saving the candidate stripes to the output directory in a .tsv file. They should then be filtered by the user.

It is recommended to use the default values of all parameters specified in usage options (python -m gstripe.gstripe --help).

Use --fix_bin_start in case of binned data, where adjacent bins would overlap (i.e. when one anchor end is "15000" and the start of an adjacent anchor is also "15000"). Recommended for HiChIP.

In case of problems with multiprocessing, use --max_workers=1