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Tool for motif conservation analysis

Project Description

MoCA: Tool for MOtif Conservation Analysis

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Python rewrite of `MoCA0.1.0`_


API Documentation

``moca`` is most compatible with the `conda`_ environment.


$ git clone
$ cd moca
$ conda create env -f environment.yml python=2.7
$ source activate mocatest
$ pip install .

A sample configuration file is available: `tests/data/application.cfg`


MoCA makes use of PhyloP/PhastCons/GERP scores to assess the quality of a
motif, the hypothesis being a 'true motif' would evolve slower as compared
to its surrounding(flanking sequences).

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$ mocacli --help
Usage: mocacli [OPTIONS]

Run moca

-i, --bedfile TEXT Bed file input [required]
-o, --oc TEXT Output Directory
-c, --configuration TEXT Configuration file [required]
--flank-seq INTEGER Flanking sequence length [required]
--flank-motif INTEGER Length of sequence flanking motif [required]
-g, -gb, --genome-build TEXT Key denoting genome build to use in
configuration file [required]
--help Show this message and exit.



$ mocacli -i tests/data/ENCFF002CDP.ctcf.bed\
-g hg19
-c tests/data/application.cfg\
-o output_dir

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``moca`` is mostly extensively tested. See `code-coverage`_.

Run tests locally


$ ./


This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _`MoCA0.1.0`:
.. _Cookiecutter:
.. _`audreyr/cookiecutter-pypackage`:
.. _`conda`:
.. _`code-coverage`:


0.1.0 (2016-02-22)

* First release on PyPI.

Release History

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