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 saccharomyces_cerevisiae as sgmygene = sg.stdgenes["XKS1"]mygenemygene.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.sysgenes["YGR194C"]mygene.cds()Dseqrecord(-1803)
mygene.locus()Dseqrecord(-3803)
mygene.promoter()Dseqrecord(-1006)
mygene.terminator()Dseqrecord(-331)
mygene.downstream_gene()mygene.upstream_gene()mygene.deletion_cassettes()[Cassette(outer_cassette=Amplicon(1671), inner_cassette=Amplicon(1617), UPTAG=UPTAG_primer_YGR194C 74-mer:5'-GAGATTAGTACTTTA..GAC-3', DNTAG=DNTAG_primer_YGR194C 74-mer:5'-TTATTCAAACATATT..TCG-3', UPstream45=UPstream45_YGR194C 45-mer:5'-CCCTCTCGAGAAAAA..ATG-3', DNstream45=DNstream45_YGR194C 45-mer:5'-TGTGTGTACTTGTCA..TTA-3')]
mygene.deletion_loci()[Contig(-3587)]
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 |
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.
- Python 3.7 - 3.9 (pygenome version 0.9.0 was the last to support Python 2.7.)
- pydna
- requests
- appdirs
The second best way of installing pygenome is by using pip
sudo pip install pygenome
pydna source code is hosted on Github.