Accessing the Saccharomyces cerevisiae genome from Python
Project description
Pygenome provide a module for accessing the Saccharomyces cerevisiae genome from Python. Genes, promoters, terminators and intergenic sequences are available by systematic names (like YPR080w) or by standard name. DNA sequences are returned as Biopython SeqRecord objects. Biopython, percache and appdirs are required for installation.
Typical usage at the command line could look like this:
>>> from pygenome import sg
>>> sg.locus("TEF1")
SeqRecord(seq=Seq('CTTCATCGGTATCTTCGCTATATTCTTTTTAGTCGAATTTGCGGGGAGAAGATG...AAC', IUPACAmbiguousDNA()), id='BK006949.2', name='BK006949', description='TPA: Saccharomyces cerevisiae S288c chromosome XVI.', dbxrefs=[])
>>> sg.locus("YPR080w")
SeqRecord(seq=Seq('CTTCATCGGTATCTTCGCTATATTCTTTTTAGTCGAATTTGCGGGGAGAAGATG...AAC', IUPACAmbiguousDNA()), id='BK006949.2', name='BK006949', description='TPA: Saccharomyces cerevisiae S288c chromosome XVI.', dbxrefs=[])
>>> a=sg.locus("TEF1")
>>> b=sg.locus("YPR080w")
>>> str(a.seq) == str(b.seq)
True
>>> prom=sg.promoter("TEF1")
>>> prom
SeqRecord(seq=Seq('ACAATGCATACTTTGTACGTTCAAAATACAATGCAGTAGATATATTTATGCATA...AAA', IUPACAmbiguousDNA()), id='BK006949.2', name='BK006949', description='TPA: Saccharomyces cerevisiae S288c chromosome XVI.', dbxrefs=[])
>>> term=sg.terminator("TEF1")
>>> term
SeqRecord(seq=Seq('GGAGATTGATAAGACTTTTCTAGTTGCATATCTTTTATATTTAAATCTTATCTA...CAG', IUPACAmbiguousDNA()), id='BK006949.2', name='BK006949', description='TPA: Saccharomyces cerevisiae S288c chromosome XVI.', dbxrefs=[])
NEWS
version |
date |
comment |
|---|---|---|
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.x
Versions other than 2.7 has not been tried with this software. Version 2.7.3 was used to build the distribution.
Python 3.x
This code has not been tested with python 3.
Installation
Source
Open the pydna source code directory (containing the setup.py file) in terminal and type:
sudo python setup.py install <enter>
If you need to do additional configuration, e.g. changing the base directory, please type python setup.py, or see the documentation for Setuptools.
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
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