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Simple access to the reference genomes at UCSC

Project Description

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

Release History

Release History

This version
History Node

0.1

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
ucscgenome-0.1.zip (9.0 kB) Copy SHA256 Checksum SHA256 Source Jun 12, 2013

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