omicexperiment 0.1.2.dev1

Example code

from omicexperiment.experiment.microbiome import MicrobiomeExperiment
from omicexperiment.filters import Sample, Taxonomy

mapping = "example_map.tsv"
biom = "example_fungal.biom"
tax = "blast_tax_assignments.txt"

#our Experiment object
exp = MicrobiomeExperiment(biom, mapping,tax)

#include only samples with more than 90000 counts
exp.filter(Sample.count > 90000)

##collapse the OTUs in the _data_ DataFrame to genus level assignment
exp.filter(Taxonomy.groupby('genus')) #any taxonomic rank can be passed

Installation

Just clone the git repository. Hopefully very shortly, the package will be uploaded to PyPi and will be pip-installable.

Due to bugs in handling numpy installation in setuptools, it is better to install numpy first using ‘pip install numpy’.

Dependencies

Current omicexperiment dependencies:

• numpy

• scipy

• pandas

• scikit-bio

• biom-format

• lxml

• pygal

License

This package is released as open-source, under a BSD License. Please see COPYING.txt.

Documentation

Please see the doc folder in the package (https://github.com/bassio/omicexperiment/tree/master/doc), it contains Jupyter notebooks that runs you through most of the current package functionality.

Acknowledgements

Thank you to all the great python bioinformatics and data science community for releasing their code as open source.

Contributing and use in your research

Please be advised that at this stage, this package is still alpha software. Testing is still not implemented so be careful. But if you are interested in contributing to this project, please contact. Contributors are welcome to improve the software. Nowadays, I expect the package to continue growing slowly as I add functionality and improvements as long as I need it in my own research. I will be initially focusing on developing the MicrobiomeExperiment part.

0.1.2-dev

• Development version(s) dedicated to fixing PyPI installation.

0.1.1

• Initial version