pararead 0.8.1

Parallel processing of sequencing reads

# Pararead: parallel processing of sequencing reads

Pararead is a python package that simplifies parallel processing of DNA sequencing reads (BAM or SAM files), by parallelizing across chromosomes. Pararead is built for developers of python scripts that process data read-by-read. It enables you to quickly and easily parallelize your script.

## Install

Pararead is hosted on pypi. Install with:

`console pip install pararead `

## Minimum working example

In the [examples](https://github.com/databio/pararead/tree/master/examples) folder you can find count_reads.py, which will count the number of reads in a sam/bam file in parallel.

Run this on your bam file like this:

` python examples/count_reads.py file.bam -O output.txt --cores 2 `

Look at the code to see how this is implemented.

## Developing tools that use pararead

The main model provided is an abstract class called ParaReadProcessor, for which concrete children are created by implementing a __call__ method. This creates a callable instance that is then mapped over chromosomes.

The concept is generally described in this early [blog post](http://databio.org/posts/tabix_files.html), which initiated the project that eventually became pararead.