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McIntyre Library

This is a set of simple classes to handle various types of genomic/transcriptomic data. Some of these classes are wrappers for other python modules such as gffutils. In order to use these classes various python modules will need to be installed. Including:

  • cPickle
  • numpy
  • pandas
  • matplotlib
  • pysam
  • gffutils
  • pyvcf

I suggest using this repository as a subtree in your project. This will allow you to pull changes to mclib_Python while the project is active. But then have a code freeze once the project is published, so that you can easily tell what code was run. First setup you project's scripts folder as a git repository. Then to subtree this library do the following inside of your scripts folder.

Add the mclib_Python remote

$ git remote add mclib_Python git@github.com:McIntyre-Lab/mclib_Python.git

Create the Subtree

$ git subtree add --prefix=mclib_Python --squash mclib_Python master

To pull updates from upstream

$ git subtree pull --prefix=mclib_Python --squash mclib_Python master

To push updates to upstream

$ git subtree push --prefix=mclib_Python --squash mclib_Python master

For more detailed information about this library please see McIntyre Library Documentation