https://github.com/coderefinery/word-count

Example project we use in the reproducibility lesson.
https://github.com/coderefinery/word-count

Last synced: 5 months ago
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Example project we use in the reproducibility lesson.

• Host: GitHub
• URL: https://github.com/coderefinery/word-count
• Owner: coderefinery
• License: mit
• Created: 2019-06-11T21:40:48.000Z (about 7 years ago)
• Default Branch: main
• Last Pushed: 2024-09-19T06:08:25.000Z (over 1 year ago)
• Last Synced: 2025-09-10T04:46:43.150Z (9 months ago)
• Language: Python
• Homepage:
• Size: 850 KB
• Stars: 8
• Watchers: 3
• Forks: 53
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
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# Word count example

This example project will count words in a given text and plot a bar chart of the 10

most common words.

![](https://coderefinery.github.io/reproducible-research/_images/arrows.png)

## Dependencies

See `environment.yml`.

## Usage

In this example we wish to: 

1. Analyze word frequencies using [statistics/count.py](https://github.com/coderefinery/word-count/blob/main/statistics/count.py)

   for 4 books (they are all in the [data](https://github.com/coderefinery/word-count/tree/main/data) directory).

2. Plot a histogram using [plot/plot.py](https://github.com/coderefinery/word-count/blob/main/plot/plot.py)

For one book (`isles.txt`) use the scripts like this:

```

$ python code/count.py data/isles.txt > statistics/isles.data

$ python code/plot.py --data-file statistics/isles.data --plot-file plot/isles.png

```

To run these scripts for all books you can collect these calls all into one bash script and run it with `bash run_all.sh`. 

One step further and less code, you could also loop through all known book titles in a bash script and run it with: `bash run_all_loop.sh`.

### Workflow

Implemented using Snakemake in `Snakefile`.

### Tests

End to end tests are provided in the test directory.

## Acknowledgement

Inspired by and derived from https://hpc-carpentry.github.io/hpc-python/

  which is distributed under

  [Creative Commons Attribution license (CC-BY 4.0)](https://creativecommons.org/licenses/by/4.0/).

## CodeRefinery workshop

We use this example in the CodeRefinery workshop in this lesson:

- https://coderefinery.github.io/reproducible-research/