ucscgenome 0.1

Simple access to the reference genomes at UCSC

The package allows to easily download and use genomic data at UCSC. This is essentially a thin “caching” wrapper around the twobitreader library.

Installation

The simplest way to install the package is via easy_install or pip:

$ easy_install ucscgenome

Dependencies

• twobitreader

Usage

The primary usage example is the following:

from ucscgenome import Genome
g = Genome('sacCer2')
print str(g['chrI'][0:100])

On the second line of the above example the following steps are performed:

• The local cache directory is searched for the pre-downloaded genome data. If the data is readily available, it is opened for reading.

• If there is not cached version of the sacCer2 genome, it is downloaded from the UCSC site to the cache directory.

• The local data is downloaded and stored using the compact 2bit format.

You can configure the details of the procedure by providing additional options to the Genome constructor:

g = Genome('hg19', cache_dir='my_genomes', use_web=False)

which means that the genome data is to be searched for in the ./my_genomes directory and in no case should a download be attempted, or:

g = Genome('hg19', source_url_pattern='http://my.site.com/genomes/%(id)s/%(id)s.2bit')

which means that the genomic data is to be downloaded from your own server rather than UCSD’s.

See also

• Report issues and submit fixes at Github: https://github.com/konstantint/ucscgenome

Related packages

• http://pyucsc.readthedocs.org/

• https://pypi.python.org/pypi/twobitreader

• https://pypi.python.org/pypi/pyfasta

• https://pypi.python.org/pypi/cruzdb

• https://pypi.python.org/pypi/pyliftover