Accessing the Saccharomyces cerevisiae genome from Python
Project description
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.
Typical usage at the IPython command line could look like this:
from pygenome import sg
sg.gene["TEF1"]
Out[2]: yeast gene YPR080W
sg.gene["TEF1"].cds()
Out[3]: SeqRecord(seq=Seq('ATGGGTAAAGAGAAGTCTCACATTAACGTTGTCGTTATCGGTCATGTCGATTCT...TAA', IUPACAmbiguousDNA()), id='BK006949.2', name='BK006949', description='BK006949 REGION: 700594..701970', dbxrefs=[])
sg.gene["TEF1"].locus()
Out[4]: SeqRecord(seq=Seq('CTTCATCGGTATCTTCGCTATATTCTTTTTAGTCGAATTTGCGGGGAGAAGATG...AAC', IUPACAmbiguousDNA()), id='BK006949.2', name='BK006949', description='BK006949 REGION: 699594..702970', dbxrefs=[])
sg.gene["TEF1"].promoter()
Out[5]: SeqRecord(seq=Seq('ACAATGCATACTTTGTACGTTCAAAATACAATGCAGTAGATATATTTATGCATA...AAA', IUPACAmbiguousDNA()), id='YPR079W_YPR080W', name='.', description='BK006949 REGION: 700015..700593', dbxrefs=[])
sg.gene["TEF1"].deletion_locus()
Out[6]: 'No deletion primers available!'
sg.gene["CYC1"].deletion_locus()
Out[7]: SeqRecord(seq=Seq('GAGGCACCAGCGTCAGCATTTTCAAAGGTGTGTTCTTCGTCAGACATGTTTTAG...GTG', IUPACAmbiguousDNA()), id='yjr048w::KanMX4 locus with 1000 bp up and 1000 bp downstream DNA', name='yjr048w::KanMX4', description='<unknown description>', dbxrefs=[])
version |
date |
comment |
|---|---|---|
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 |
System Requirements
Python 2.7
Version 0.9.0 was the last one to support Python 2.7.
Installation
Source
The best way of installing pygenome is by using pip
sudo pip install pygenome
Source Code Repository
pydna source code is hosted on Github:
Distribution Structure
README.rst – This file.
LICENSE.txt – What you can do with the code.
MANIFEST.in – Tells distutils what files to distribute
setup.py – Installation file.
pygenome/ – The actual code.
docs/ – Documentation.
scripts/ – Miscellaneous perhaps useful scripts
tests/ – Testing code
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
