blacktie 0.2.1.2

A python wrapper for analysis of RNA-seq data with the popular tophat/cufflinks pipeline.

Welcome to Blacktie!
==========================

This package is functional but under heavy development so you may want to periodically
pull the latest code from the repo at git://github.com/xguse/blacktie.git.

For the **LATEST** version pull the 'develop' branch.

**I seek collaboration and contributions to improve this tool.**

**PLEASE** take it and run with it, but send me your progress!

Its goal is to **simplify the integration of all the
input/output streams of the tophat/cufflinks workflow** into a single yaml based config
file and automate as much of everything else as possible so that once the config file
is filled out, **the entire process of analysing a multi-condition RNA-seq experiment can
be run with a single command.**

I have not had time to fill in ALL the doc strings but updating them regularly.

(Current version of the docs can be found here: http://xguse.github.com/blacktie/)

If you want to use/contribute before the docs are complete, please feel free to contact me at
[e-mail] for guidance.

Issue tracking
--------------
If you find issues, bugs, or have feature requests, please go here to submit them: https://github.com/xguse/blacktie/issues


Blacktie Poster
------------------------


.. raw:: html
<iframe src="http://wl.figshare.com/articles/714149/embed?show_title=1" width="568" height="200" frameborder="0"></iframe>


To credit the use of blacktie please cite the poster using the DOI link provided.

*Introducing Blacktie: a simpler way to do RNA-seq using Tophat/Cufflinks/CummeRbund*. Augustine Dunn. figshare.
http://dx.doi.org/10.6084/m9.figshare.714149



Usage
-----
.. code-block:: none

usage: blacktie [-h] [--version]
[--prog {tophat,cufflinks,cuffmerge,cuffdiff,cummerbund,all}]
[--hide-logs] [--no-email]
[--mode {analyze,dry_run,qsub_script}]
config_file

This script reads options from a yaml formatted file and organizes the
execution of tophat/cufflinks runs for multiple condition sets.

positional arguments:
config_file Path to a yaml formatted config file containing setup
options for the runs.

optional arguments:
-h, --help show this help message and exit
--version Print version number.
--prog {tophat,cufflinks,cuffmerge,cuffdiff,cummerbund,all}
Which program do you want to run? (default: tophat)
--hide-logs Make your log directories hidden to keep a tidy
'looking' base directory. (default: False)
--no-email Don't send email notifications. (default: False)
--mode {analyze,dry_run,qsub_script}
1) 'analyze': run the analysis pipeline. 2) 'dry_run':
walk through all steps that would be run and print out
the command lines; however, do not send the commands
to the system to be run. 3) 'qsub_script': generate
bash scripts suitable to be sent to a compute
cluster's SGE through the qsub command. (default:
analyze)





Credits
-------

- `Distribute`_
- `Buildout`_
- `modern-package-template`_

.. _Buildout: http://www.buildout.org/
.. _Distribute: http://pypi.python.org/pypi/distribute
.. _`modern-package-template`: http://pypi.python.org/pypi/modern-package-template


.. image:: https://d2weczhvl823v0.cloudfront.net/xguse/blacktie/trend.png
:alt: Bitdeli badge
:target: https://bitdeli.com/free


.. This is your project NEWS file which will contain the release notes.
.. Example: http://www.python.org/download/releases/2.6/NEWS.txt
.. The content of this file, along with README.rst, will appear in your
.. project's PyPI page.

News
====

0.2.1.2
-----------
*Release date: 2013-07-17*

* version number system adopted to conform to PEP386
* This is a hot fix to squash a bug described in github issue: https://github.com/xguse/blacktie/issues/10
* **in short:** on a Mac ``pprocess`` complained "AttributeError: 'module' object has no attribute 'poll'" when trying to set up a queue.
* the quick fix is to look for that exception and continue without ``pprocess`` if encountered to avoid the fatal exception.



0.2.1
---------
*Release date: 2013-05-15*

* git tag: 'v0.2.1'
* added new script named blacktie-cummerbund to run cummeRbund
* added new class in calls.py CummerbundCall to use blacktie-cummerbund script to add cummeRbund plots to blacktie script
* checks for R and rpy2 installations
* if cummeRbund R library not found, it walks you through installing it
* ``src/blacktie/utils/calls.py``: - fixed _flag_out_dir() so that if the outdir has not been created yet it gracefully moves on
* ``examples/blacktie_config_example.yaml``: - added cummerbund_options
* ``requirements.txt``: - added rpy2
* updated docs

0.2.0rc1
--------

*Release date: 2013-04-19*

* git tag: 'v0.2.0rc1'
* Added support for handling biological replicates in cuffdiff runs.
* Major changes to yaml config:
* condition_queue[index].group_id --> condition_queue[index].experiment_id
* addition of condition_queue[index].replicate_id to track replicate data
* condition_queue[index].name now represents description of an 'experiemental condition' and will be shared by replicates.


0.1.1
-----

*Release date: 2013-03-21*

* git commit SHA digest: 9d7c02d5e7f4ec8970bb2291c3eb6ff8f4dbe542
* git tag: 'v0.1.1'


0.1_dev
-------

*Release date: 2013-03-20*

* git commit SHA digest: 808c11fb396c71af55ff690fa6f2e628e5ffd758
* git tag: 'v0.1-dev'
* First uploaded to PyPI
* This verion is still under active development.