Metadata-Version: 1.1
Name: pyopossum3
Version: 0.1
Summary: SQLAlchemy-based interface to the oPOSSUM3 transcription factor binding database.
Home-page: https://github.com/konstantint/pyopossum3
Author: Konstantin Tretyakov
Author-email: kt@ut.ee
License: MIT
Description: =====================================================================================
        SQLAlchemy-based interface to the oPOSSUM3 transcription factor binding site database
        =====================================================================================
        
        The package provides an object-oriented access interface to the `oPOSSUM3 <http://opossum.cisreg.ca/oPOSSUM3/>`_ raw database tables.
        
        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 <http://opossum.cisreg.ca/oPOSSUM3/download.html>`_ 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
        
        
Keywords: bioinformatics oPOSSUM3 data-access transcription tfbs
Platform: Platform Independent
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
