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Accessing the Saccharomyces cerevisiae genome from Python

Project description

# [![icon](SuperYeast.jpg)]( [pygenome](

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Harness the awesome power of yeast genetics through python! Pygenome provide access to the [Saccharomyces cerevisiae](
genome from Python. [Genes](,
[terminators](, and
[intergenic](, sequences
as well as the deletion [loci]( created by the
[genome wide deletion project](
are available by their systematic names (like [YPR080w]( or by
standard name (like [CYC1]( DNA
sequences are returned as Biopython
[SeqRecord]( objects. Thanks to [SGD]( for letting me use the SuperYeast logotype above.

Typical usage at the [IPython]( command line could look like this:

from pygenome import sg

mygene = sg.stdgene["XKS1"]

Out[3]: Gene XKS1/YGR194C

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

Out[5]: Gene XKS1/YGR194C

Out[6]: SeqRecord(seq=Seq('ATGTTGTGTTCAGTAATTCAGAGACAGACAAGAGAGGTTTCCAACACAATGTCT...TAA', IUPACAmbiguousDNA()), id='BK006941.2', name='BK006941', description='BK006941 REGION: complement(887876..886072)', dbxrefs=[])
Out[7]: SeqRecord(seq=Seq('ATCCTGCTGTAGTTATGGCACTAAAGTTTTTTTGTAAATCTTTTTATATGTTAA...GAA', IUPACAmbiguousDNA()), id='BK006941.2', name='BK006941', description='BK006941 REGION: complement(888876..885072)', dbxrefs=[])

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

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=[])

Out[10]: Gene PDX1/YGR193C

Out[11]: Gene SKI6/YGR195W

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]( or [Miniconda]( 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]( 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]( (pygenome version 0.9.0 was the last to support Python 2.7.)
- [pydna](
- [requests](
- [appdirs](

## Install with pip

The second best way of installing pygenome is by using

sudo pip install pygenome

### Source Code Repository

pydna source code is hosted on [Github](

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