Skip to main content
This is a pre-production deployment of Warehouse. Changes made here affect the production instance of PyPI (pypi.python.org).
Help us improve Python packaging - Donate today!

Accessing the Saccharomyces cerevisiae genome from Python

Project Description
# [![icon](SuperYeast.jpg)](http://www.yeastgenome.org/) [pygenome](https://pypi.python.org/pypi/pygenome)

[![Build Status](https://travis-ci.org/BjornFJohansson/pygenome.svg?branch=master)](https://travis-ci.org/BjornFJohansson/pygenome)
[![Build status2](https://ci.appveyor.com/api/projects/status/aplxufiixw124dvr?svg=true)](https://ci.appveyor.com/project/BjornFJohansson/pygenome)
[![Codeship Status for BjornFJohansson/pygenome](https://app.codeship.com/projects/f461d290-71e3-0135-828b-52ef08dd0262/status?branch=master)](https://app.codeship.com/projects/243478)
[![codecov](https://codecov.io/gh/BjornFJohansson/pygenome/branch/master/graph/badge.svg)](https://codecov.io/gh/BjornFJohansson/pygenome)
[![Documentation Status](https://readthedocs.org/projects/pygenome/badge/?version=latest)](http://pygenome.readthedocs.io/en/latest/?badge=latest)
[![PyPI version](https://badge.fury.io/py/pygenome.svg)](https://badge.fury.io/py/pygenome)
[![Anaconda-Server Badge](https://anaconda.org/bjornfjohansson/pygenome/badges/version.svg)](https://anaconda.org/bjornfjohansson/pygenome)

Harness the awesome power of yeast genetics through python! Pygenome provide access to the [Saccharomyces cerevisiae](https://microbewiki.kenyon.edu/index.php/Saccharomyces_cerevisiae)
genome from Python. [Genes](http://en.wikipedia.org/wiki/Gene),
[promoters](http://en.wikipedia.org/wiki/Promoter_(genetics)),
[terminators](http://en.wikipedia.org/wiki/Terminator_(genetics)), and
[intergenic](http://en.wikipedia.org/wiki/Intergenic_region), sequences
as well as the deletion [loci](http://en.wikipedia.org/wiki/Locus_(genetics)) created by the
[genome wide deletion project](http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html)
are available by their systematic names (like [YPR080w](http://www.yeastgenome.org/locus/S000006284/overview)) or by
standard name (like [CYC1](http://www.yeastgenome.org/locus/S000003809/overview)). DNA
sequences are returned as Biopython
[SeqRecord](http://biopython.org/wiki/SeqRecord) objects. Thanks to [SGD](http://www.yeastgenome.org/) for letting me use the SuperYeast logotype above.

Typical usage at the [IPython](http://ipython.org/) command line could look like this:

from pygenome import sg

mygene = sg.stdgene["XKS1"]

mygene
Out[3]: Gene XKS1/YGR194C

mygene.short_description
Out[4]: Xylulokinase; converts D-xylulose and ATP to xylulose 5-phosphate and ADP; rate limiting step in fermentation of xylulose; required for xylose fermentation by recombinant S. cerevisiae strains

sg.sysgene["YGR194C"]
Out[5]: Gene XKS1/YGR194C

mygene.cds
Out[6]: SeqRecord(seq=Seq('ATGTTGTGTTCAGTAATTCAGAGACAGACAAGAGAGGTTTCCAACACAATGTCT...TAA', IUPACAmbiguousDNA()), id='BK006941.2', name='BK006941', description='BK006941 REGION: complement(887876..886072)', dbxrefs=[])

mygene.locus()
Out[7]: SeqRecord(seq=Seq('ATCCTGCTGTAGTTATGGCACTAAAGTTTTTTTGTAAATCTTTTTATATGTTAA...GAA', IUPACAmbiguousDNA()), id='BK006941.2', name='BK006941', description='BK006941 REGION: complement(888876..885072)', dbxrefs=[])

mygene.promoter
Out[8]: SeqRecord(seq=Seq('ATGATGATCCTGCTGTAGTTATGGCACTAAAGTTTTTTTGTAAATCTTTTTATA...TTA', IUPACAmbiguousDNA()), id='YGR195W_YGR194C', name='.', description='BK006941.2 REGION: complement(887876..888881)', dbxrefs=[])

mygene.terminator
Out[9]: SeqRecord(seq=Seq('AATATGTTTGAATAATTTATCATGCCCTGACAAGTACACACAAACACAGACACA...AAA', IUPACAmbiguousDNA()), id='YGR194C_YGR195W', name='.', description='Intergenic sequence between upstream gene YGR194C and downstream gene Gene PDX1/YGR193C', dbxrefs=[])

mygene.downstream_gene
Out[10]: Gene PDX1/YGR193C

mygene.upstream_gene
Out[11]: Gene SKI6/YGR195W

mygene.deletion_locus
Out[12]: SeqRecord(seq=Seq('ATCCTGCTGTAGTTATGGCACTAAAGTTTTTTTGTAAATCTTTTTATATGTTAA...GAA', IUPACAmbiguousDNA()), id='ygr194c::KanMX4 locus with 1000 bp up and 1000 bp downstream DNA', name='ygr194c::KanMX4', description='description?', dbxrefs=[])

| ver | date | comment |
|-------|------------|-----------------------------------------------------|
| 2.0.0 | 2017-09-02 | split sg.gene dict into sg.stdgene and sg.sysgene |
| 1.0.0 | 2017-03-24 | Internal stuff, automativ build & test |
| 0.9.5 | 2017-01-01 | Python 3 release |
| 0.9.0 | 2015-05-01 | Changed interface to a more object oriented style |
| 0.5.0 | 2015-03-03 | Documentation, automatic build, test and deployment |
| 0.0.6 | 2014-06-17 | Bugfix |
| 0.0.5 | 2014-06-14 | Simpler api (see example above) |
| 0.0.1 | 2013-08-01 | first release |

## Installation using conda on Anaconda

The absolutely best way of installing and using pygenome is to use the
free [Anaconda](https://store.continuum.io/cshop/anaconda) or [Miniconda](http://conda.pydata.org/miniconda.html) python distributions.

Anaconda is a large download (about 400 Mb) while Miniconda is about 40-50 Mb.

Once Anaconda (or Miniconda) is installed, the conda package manager can be used to install pygenome
from the [BjornFJohansson](https://anaconda.org/bjornfjohansson) package channel.

The first step is to add the channel by typing the command below followed by return:

conda config --append channels BjornFJohansson

Then pygenome can be installed by typing the command below followed by return:

conda install pygenome

This works on Windows, MacOSX and Linux, and installs all necessary dependencies automatically.

## Requirements

- [Python 3.5 or 3.6](http://www.python.org) (pygenome version 0.9.0 was the last to support Python 2.7.)
- [pydna](http://pypi.python.org/pypi/pydna)
- [requests](http://pypi.python.org/pypi/requests)
- [appdirs](https://pypi.python.org/pypi/appdirs)

## Install with pip

The second best way of installing pygenome is by using
[pip](https://packaging.python.org/en/latest/installing.html#installing-from-pypi)

sudo pip install pygenome

### Source Code Repository

pydna source code is hosted on [Github](https://github.com/BjornFJohansson/pygenome).


Release History

Release History

This version
History Node

2.0.0

History Node

1.0.2

History Node

1.0.0

History Node

1.0.0a18

History Node

1.0.0a17

History Node

1.0.0a16

History Node

1.0.0a15

History Node

1.0.0a14

History Node

1.0.0a12

History Node

1.0.0a11

History Node

1.0.0a10

History Node

0.9.5

History Node

0.9.0

History Node

0.5.0

Download Files

Download Files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
pygenome-2.0.0-py3.5.egg (12.1 MB) Copy SHA256 Checksum SHA256 3.5 Egg Dec 11, 2017
pygenome-2.0.0-py3.6.egg (12.1 MB) Copy SHA256 Checksum SHA256 3.6 Egg Dec 11, 2017
pygenome-2.0.0-py3-none-any.whl (12.1 MB) Copy SHA256 Checksum SHA256 py3 Wheel Dec 11, 2017
pygenome-2.0.0.zip (12.1 MB) Copy SHA256 Checksum SHA256 Source Dec 11, 2017

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting