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Tutorial

Introduction

ezTracks only needs a configuration file to work. The only options implemented are the same as the sample file test/test_config.ini. The coordinates must be in bed format.

To process to generate a plot is:

  1. Activate the eztracks environment (or having all dependencies available in the PATH)
  2. Run python eztracks.py check path/to/config_file
  3. Run python eztracks.py prepare path/to/config_file
  4. Run python eztracks.py draw path/to/config_file
  5. Modify output_path/config.ini for cosmetic changes and rerun the pyGenomeTracks command.

1. Check the integrity of the test data

We are going to work with the test data provided in this repository (they are cropped to the region of interest of the configuration file, so you may want to try with your own data after finishing this tutorial). In your terminal enter this folder, and examine the configuration file.

# TO UPDATE
> cat test_config/config.ini

Now, we are going to activate the environment and verify the config file and the input data:

# TO UPDATE
> conda activate eztracks
> python eztracks.py check test_config/test_config.ini

2. Preprocess track files

If there were no errors in the last step, now we can preprocess the input tracks. Basically we will get only the portion we are interested to plot into the folder output_path/prep:

> python eztracks.py prepare test/test_config.ini
# TO UPDATE

3. Plot the tracks

# TO UPDATE
> python eztracks.py draw test/test_config.ini

And now the plot is ready in test_output/my_tracks.pdf! As the terminal output indicates, you can modify test_output/config.ini and rerun the pyGenomeTracks command to redraw the plot. The possible parameters for this new configuration file are located at https://pygenometracks.readthedocs.io/en/latest/content/possible-parameters.html

output plot