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pypblat

A python-driven wrapper for pblat

This program uses Python 3.6 with pipenv. If you don't have pipenv, you can install it following the instructions here.
To install the program:

  1. Clone this repository
  2. run make sharedlib in the repository's root directory
  3. run pipenv install --dev from the repository's root directory.
  4. run pipenv shell to activate the python environment

To run the program:

  1. There is a pypblat program that is now on your path. Run pypblat --help to see the available commands. For now there's only one, copy-count. You can run pypblat copy-count --help to see the available flags for that program.
  2. A sample run could look like:
pypblat copy-count /mnt/nas/Shared/Nate/COPIA_DM_copies_plus_shCopia.fa /mnt/nas/Shared/Nate/clipped.fasta