Simple script for colleagues to use for batching repeat counts into specified groups. Useful in low read-count situations, for further data analysis.
It is best practice to ensure your version of 'setuptools' is up-to-date before trying anything. If you are not using an administrator account currently, you may need to use sudo.
$ easy_install -U setuptools
And for proper package installation:
$ cd ~/src/
$ python setup.py install
Here's how to use it for now. To launch the program when installed, launch via terminal:
$ groupie -flags
All flags for the application are:
-sam :: A path to a sam file, or a folder of sam files as input
-rng :: A numerical range to batch reads into [Default is 0-10]
-cpu :: Number of CPU threads to utilise [Default is maximum]
-out :: A path to a desired output folder [Default is $HOME/Groupie/out/]