pygenome 1.0.0a11

Accessing the Saccharomyces cerevisiae genome from Python

pygenome
========

|Build Status|\ |Coverage Status|\ |Documentation Status|

Pygenome provide access to the `Saccharomyces
cerevisiae <https://microbewiki.kenyon.edu/index.php/Saccharomyces_cerevisiae>`__
genome from Python. `Genes <http://en.wikipedia.org/wiki/Gene>`__,
`promoters <http://en.wikipedia.org/wiki/Promoter_(genetics)>`__,
`terminators <http://en.wikipedia.org/wiki/Terminator_(genetics)>`__,
and `intergenic <http://en.wikipedia.org/wiki/Intergenic_region>`__,
sequences as well as the deletion
`loci <http://en.wikipedia.org/wiki/Locus_(genetics)>`__ created by the
`genome wide deletion
project <http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html>`__
are available by their systematic names (like
`YPR080w <http://www.yeastgenome.org/locus/S000006284/overview>`__) or
by standard name (like
`CYC1 <http://www.yeastgenome.org/locus/S000003809/overview>`__). DNA
sequences are returned as Biopython
`SeqRecord <http://biopython.org/wiki/SeqRecord>`__ objects.

Typical usage at the `IPython <http://ipython.org/>`__ 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 |
+=========+==============+=======================================================+
| 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 <https://store.continuum.io/cshop/anaconda>`__ or
`Miniconda <http://conda.pydata.org/miniconda.html>`__ 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 <https://anaconda.org/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 <http://www.python.org>`__ (0.9.0 was the last to support
Python 2.7.)
- `pydna <http://pypi.python.org/pypi/pydna>`__
- `percache <http://pypi.python.org/pypi/percache>`__
- `appdirs <>`__

Install with pip
----------------

The second best way of installing pygenome is by using
`pip <https://packaging.python.org/en/latest/installing.html#installing-from-pypi>`__

::

sudo pip install pygenome

Source Code Repository
~~~~~~~~~~~~~~~~~~~~~~

pydna source code is hosted on
`Github <https://github.com/BjornFJohansson/pygenome>`__.

.. |Build Status| image:: https://travis-ci.org/BjornFJohansson/pygenome.svg?branch=master
:target: https://travis-ci.org/BjornFJohansson/pygenome
.. |Coverage Status| image:: https://coveralls.io/repos/github/BjornFJohansson/pygenome/badge.svg?branch=master
:target: https://coveralls.io/github/BjornFJohansson/pygenome?branch=master
.. |Documentation Status| image:: https://readthedocs.org/projects/pygenome/badge/?version=latest
:target: http://pygenome.readthedocs.io/en/latest/?badge=latest