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

Project description

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://

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:

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

Issue tracking
If you find issues, bugs, or have feature requests, please go here to submit them:


usage: blacktie [-h] [--prog {tophat,cufflinks,cuffmerge,cuffdiff,all}]
[--hide-logs] [--mode {analyze,dry_run,qsub_script}]

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
--prog {tophat,cufflinks,cuffmerge,cuffdiff,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)
--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:



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

.. _Buildout:
.. _Distribute:
.. _`modern-package-template`:

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.. This is your project NEWS file which will contain the release notes.
.. Example:
.. The content of this file, along with README.rst, will appear in your
.. project's PyPI page.


*Release date: 2013-05-15*

* git tag: 'v0.2.1'
* added new script named blacktie-cummerbund to run cummeRbund
* added new class in 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/``: - 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


*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.


*Release date: 2013-03-21*

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


*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.

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