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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:

https://github.com/BjornFJohansson/pygenome

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 History

0.9.0

This version

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

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0.5.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

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Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
pygenome-0.9.0-py2-none-any.whl (16.2 kB) Copy SHA256 Checksum SHA256 2.7 Wheel May 1, 2015
pygenome-0.9.0.tar.gz (12.5 MB) Copy SHA256 Checksum SHA256 Source May 1, 2015
pygenome-0.9.0.zip (12.8 MB) Copy SHA256 Checksum SHA256 Source May 1, 2015

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