pygenome 3.1.0

Accessing the Saccharomyces cerevisiae genome from Python

pygenome

Harness the awesome power of yeast genetics through python! Pygenome provide access to the Saccharomyces cerevisiae genome from Python. Genes, promoters, 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"]

mygene

Gene XKS1/YGR194C

mygene.short_description

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"]

Gene XKS1/YGR194C

mygene.cds

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

mygene.locus()

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

mygene.promoter

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

mygene.terminator

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

mygene.downstream_gene

Gene PDX1/YGR193C

mygene.upstream_gene

Gene SKI6/YGR195W

mygene.deletion_locus

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

http://www-sequence.stanford.edu/group/yeast_deletion_project/downloads.html

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 3.6 or 3.7 (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 pip

sudo pip install pygenome

Source Code Repository

pydna source code is hosted on Github.