pypore 0.0.4.dev20160229200706

Pythonic/Cythonic Nanopore Translocation Analysis

master branch

develop branch

Pypore

This project is for nanopore-translocation event finding/analysis. It’s written in Python, with numpy/scipy as a Matlab replacement. The gui library is pyside, and pyqtgraph is used for plotting. More information can be found here.

Note that Pypore/PyporeGui are pre-release, major changes can happen at any time.

Pull requests are welcome!

Installing

Dependencies

Pypore has the following dependencies:

• numpy

• scipy

• PyTables

PyporeGui depends on all of the above and:

• PySide

• pyqtgraph

Building from source additionally requires:

• Cython

Running the tests requires:

• nose

Installing with pip

Pypore is currently pre-release, so we’ll install with the –pre tag.

pip install pypore --pre

A new dev release is deployed with every push to the develop branch, so upgrade often!

pip install pypore --pre --upgrade

Installing from source

Clone or download the source. In the directory (with setup.py), run one of the following:

python setup.py install

or

pip install .

Running the tests:

python setup.py tests

PyporeGui

Start PyporeGui with:

import pyporegui
pyporegui.start()

License

Copyright 2014 Will Parkin

Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.