Convert genomic datatypes into Pythonic objects useful to the SciPy stack
To run the tests, download the test dataset and unpack it into plastid/test.
plastid is a Python library for genomic analysis – in particular, high-throughput sequencing data – with an emphasis on simplicity for users. It was written by Joshua Dunn in Jonathan Weissman’s lab at UCSF, initially for analysis of ribosome profiling and RNA-seq data. Versions of it have been used in several publications.
plastid’s intended audience includes computational and traditional biologists, software developers, and even those who are new to sequencing analysis. It is released under the BSD 3-Clause license.
This package provides:
- A set of scripts that implement common sequencing analyses
- A set of classes that create a simple, intuitive interfaces to genomic features, read alignments, and quantitative data. These objects readily interface with existing scientific tools, like the SciPy stack, to facilitate interactive or exploratory data analysis.
- Script writing tools that make it easy to use the objects implemented in plastid.
- Extensive documentation, both in source code and at our home page on ReadtheDocs.org.
We’re in development, so this takes a few extra steps:
Make sure you have numpy and cython installed:pip install numpy cython
Clone this repo:git clone https://github.com/joshuagryphon/plastid.git
Install dependencies:cd plastid && pip install -r requirements.txt
Build extensions:python setup.py build_ext --inplace
Install beta:python setup.py develop --user
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