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

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.