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://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
wadunn83@gmail.com 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
Usage
-----
::
usage: blacktie [-h] [--prog {tophat,cufflinks,cuffmerge,cuffdiff,all}]
[--hide-logs] [--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
--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:
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
.. raw:: html
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','//www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-39589366-1', 'github.com');
ga('send', 'pageview');
</script>
.. 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
====
0.2.0rc1
--------
*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.
==========================
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
wadunn83@gmail.com 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
Usage
-----
::
usage: blacktie [-h] [--prog {tophat,cufflinks,cuffmerge,cuffdiff,all}]
[--hide-logs] [--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
--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:
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
.. raw:: html
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','//www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-39589366-1', 'github.com');
ga('send', 'pageview');
</script>
.. 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
====
0.2.0rc1
--------
*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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
blacktie-0.2.0rc1.tar.gz
(29.3 kB
view hashes)
Built Distribution
Close
Hashes for blacktie-0.2.0rc1.linux-x86_64.exe
Algorithm | Hash digest | |
---|---|---|
SHA256 | 74cb0d202836140157f838b8b6d3d99a9232d25cc7908224e0082450488d0d16 |
|
MD5 | 6efe7538c52674ef3be947a733fba049 |
|
BLAKE2b-256 | 635b470a3d35d450ebfa95a994b67561b1889c5a8dba2ef789d71e6cb9fc46ad |