From 8e9a4ee9aca77d5eeb6903ee73d66310262a926d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micha=C5=82?= Date: Mon, 20 May 2024 10:51:45 +0200 Subject: [PATCH] Add example data file, update instructions how to run it --- README.md | 12 ++++++++---- examples/basic_test.bedpe | 16 ++++++++++++++++ 2 files changed, 24 insertions(+), 4 deletions(-) create mode 100644 examples/basic_test.bedpe diff --git a/README.md b/README.md index 2b72b9d..1e1b390 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# gSTRIPE +# gStripe Graph-based stripe caller that uses chromatin loop data. @@ -11,12 +11,16 @@ Graph-based stripe caller that uses chromatin loop data. 1. *Optional, but recommended*: Create and activate a python envrionment using [pyenv](https://github.com/pyenv/pyenv), [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [Mamba](https://mamba.readthedocs.io/en/latest/index.html). 2. Install gStripe, depending on the chosen source: - * Installing directly from github: run `pip install git+https://github.com/SFGLab/gStripe.git`. - * Installing from a zip file: run `pip install gstripe.zip` in the directory containing the downloaded file (The name of the file might differ, depending on the download source). + * Installing directly from github: run `pip install git+https://github.com/SFGLab/gStripe.git`. + * Installing from a zip file: run `pip install gstripe.zip` in the directory containing the downloaded file (The name of the file might differ, depending on the download source). + +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 -Run `python -m gstripe.gstripe input_loops_file.bedpe output_directory` to call the stripes using loops from _input_loops_file.bedpe_ and place the results and statistics in _output_directory_. +Run `python -m gstripe.gstripe input_loops_file.bedpe output_directory` to call the stripes using loops from `input_loops_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`). diff --git a/examples/basic_test.bedpe b/examples/basic_test.bedpe new file mode 100644 index 0000000..c2b54c4 --- /dev/null +++ b/examples/basic_test.bedpe @@ -0,0 +1,16 @@ +chr1 start1 end1 chr2 start2 end2 +chr20 10000 11000 chr20 20000 21000 +chr20 10000 11000 chr20 30000 31000 +chr20 10000 11000 chr20 50000 51000 +chr20 10000 11000 chr20 70000 71000 +chr20 10200 11200 chr20 50000 51000 +chr20 10200 11200 chr20 80000 81000 +chr20 20000 21000 chr20 30000 31000 +chr20 20000 21000 chr20 70000 71000 +chr20 20000 21000 chr20 70000 71000 +chr20 20000 21000 chr20 100000 101000 +chr20 20200 21200 chr20 80000 81000 +chr20 50000 51000 chr20 70000 71000 +chr21 30000 31000 chr21 80000 81000 +chr21 30000 31000 chr21 80200 81200 +chr21 40000 41000 chr21 80000 81000 \ No newline at end of file