pyopossum3 0.1 (experimental)

SQLAlchemy-based interface to the oPOSSUM3 transcription factor binding database.

Installation

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

$ easy_install pyopossum3

Dependencies

• SQLAlchemy
• MySQL-Python

Usage

A usage example is the following:

>>> from pyopossum3 import Opossum
>>> o = Opossum("mysql://opossum_r:@opossum.cmmt.ubc.ca/oPOSSUM3_human")
>>> o.ConservedTfbs.query.first().gene
>>> o.ExternalGeneId.query.filter(o.ExternalGeneId.external_id.in_(['TSPAN6'])).filter(o.ExternalGeneId.gene.has(chr='X')).first().gene
... etc ...

The second line creates a connection to the oPOSSUM server, and the third/fourth query the conserved_tfbss and external_gene_ids tables using SQLAlchemy syntax.

Naturally, for heavy analyses, you are suggested to set up your own copy of the database. See here for instructions on how to download the data.

You can get a feeling for the structure of the database by running the following:

>>> for cls in o.all_orm_classes:
>>>    print cls.query.first()

The main table you should probably care about is ConservedTfbs, which contains matches in the vicinity of each gene, annotated with match score and conservation level.

An example using the ucscgenome package to verify that TFBS sequences are indeed correct:

>>> c = o.ConservedTfbs.query.filter(o.ConservedTfbs.strand==1).first()
>>> c.gene.chr, c.absolute_start, c.absolute_end, c.seq
('X', 99890235L, 99890253L, 'AGAAACATTGCATACTGC')
>>> from ucscgenome import Genome
>>> g = Genome('hg19')
>>> g['chrX'][99890235:99890253]
'AGAAACATTGCATACTGC'

Note

The author of this package is not associated with the creators and maintainers of the oPOSSUM3 tool.

See also

• Report issues and submit fixes at Github: https://github.com/konstantint/pyopossum3