Copyright © 2018, Richard Campen. All rights reserved.
See LICENSE.txt for full license conditions.
seq-experiment is a package designed to facilitate analysis of sequencing data. It does this through the
SeqExp object which contains feature abundance counts (e.g. sequences or OTUs) along with related
classifications, metadata, and raw sequences. The SeqExp object is built on top of the pandas library,
with each of these data types stored in their own pandas DataFrames as attributes on the SeqExp object.
The SeqExp object then provides methods to easily manipulate the data within each DataFrame simultaneously
and intelligently. For example, grouping sequence abundances based on classifications, subsetting data based on
sample metadata, etc. The SeqExp object also provides some basic plotting of sequence abundance data, incorporating the
classifications and metadata.
The SeqExp object is intended to provide some of the functionality of the phyloseq object in the R package phyloseq, within a python environment.
The install the latest release run pip install seq-experiment. To install the most up to date version you should download/clone this repository and create a binary distribution using python setup.py bdist_wheel that will create
a .whl file in the dist folder. You can then install seq-experiment with pip from the .whl file using pip install <wheel_file_name>. The advantage of this method over just running python setup.py install is that you can easily
remove or update the package via pip.
This package requires the following packages to run:
- Numpy
- Pandas
- Matplotlib
An easy way to meet these dependency requirements is to install the Anaconda Python distribution.