pygenome 1.0.0a18

Accessing the Saccharomyces cerevisiae genome from 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.

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!'


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=[])

ver	date	comment
1.0.0	2017-	?
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

Installation using conda on Anaconda

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.

Requirements

• Python 3 (0.9.0 was the last to support Python 2.7.)

• pydna

• requests

• appdirs

Install with pip

The second best way of installing pygenome is by using pip

sudo pip install pygenome

Source Code Repository

pydna source code is hosted on Github.