Add example data file, update instructions how to run it

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`).

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