https://github.com/mvinyard/pool-sharq

Python wrapper for the Broad Institute GPP's poolq software
https://github.com/mvinyard/pool-sharq

crispr python

Last synced: 3 months ago
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Python wrapper for the Broad Institute GPP's poolq software

• Host: GitHub
• URL: https://github.com/mvinyard/pool-sharq
• Owner: mvinyard
• License: mit
• Created: 2021-12-11T06:42:40.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2021-12-21T05:57:49.000Z (over 3 years ago)
• Last Synced: 2025-02-28T07:52:12.488Z (3 months ago)
• Topics: crispr, python
• Language: Python
• Homepage:
• Size: 40.6 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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# pool-sharq

Python wrapper for the Broad Institute GPP's [poolq software](https://portals.broadinstitute.org/gpp/public/software/poolq)

Uses the [BeautifulSoup](https://www.crummy.com/software/BeautifulSoup/) webscraping library to check for the latest distribution of poolq from the Broad Institute's GPP. Downloads the latest distribution if it is not already downloaded.

### Install

```BASH

pip install pool_sharq

```

### Usage

```python

import pool_sharq

poolq = pool_sharq.poolq(dir="/path/to/data/") # contains rows.txt and columns.txt along with fastq files. 

poolq.run()

```

### You can also download / use test data provided by the GPP

```python

pool_sharq.download_test_data()

```

```python

poolq = pool_sharq.poolq() # point to test data

poolq.run()

```