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.
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:
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.