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pool-sharq: python interface for Broad Institute GPP's poolq software.

Project description

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pool-sharq

Python wrapper for the Broad Institute GPP's poolq software

Uses the 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

pip install pool_sharq

Usage

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

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

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