semvec/pypi-packages huggingface dataset:
timberjack 0.1.0
Logging toolbox for Python services at Mobify.
License: MIT

.. image:: https://travis-ci.org/mobify/timberjack.svg?branch=master
   :target: https://travis-ci.org/mobify/timberjack
   :alt: Travis CI Status Badge

timberjack
##########

.. image:: http://lakequip.com/wp-content/uploads/2014/05/IMG_3865.jpg
   :alt: Timberjack Tractor


Install
-------

You can install ``timberjack`` directly from the Github repo using::

    $ pip install https://github.com/mobify/timberjack/archive/master.zip


Setup in Django
---------------

TBD.


Setup in Flask
--------------

The timberjack logging tools come with a convenience class that allows the easy
configuration of a Flask application to use logging::

    from timberjack.contrib.flask import Timberjack

    ...

    app = Flask(__name__)
    timberjack = Timberjack(app)

    ...

    log = timberjack.get_logger('my.logger')



License
-------

This code is licensed under the `MIT License`_.

.. _`MIT License`: https://github.com/mobify/timberjack/blob/master/LICENSE
cbs 1.0.0
List coverage blind spots
License: MIT

Coverage Blind Spots
====================

This software lists all positions in given bam files, that have no or only 
very limited coverage and stores the result in a hdf5 file.

Usage
-----

::

    cbs [-h] [--min-cov MIN_COV] files [files ...] output

If multiple files are given, a position is designated a blind spot, if no file
contains a coverage of at least MIN_COV at this position.

Output
------

The output is a hdf5 file with the following structure. For every chromosome a 
group is created, that contains a dataset called `missing_cov`. The dataset 
contains rows of tuples of 32bit integer, representing the first blind spot and
the first position having enough coverage.

Install
-------

This software requires python3, samtools, hdf5, numpy and h5py. All python 
dependencies can be installed by installing cbs via pip::

    pip install cbs