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.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
Project details
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