optmage

Scripts for designing oligos and primers for MAGE (Multiplex Automated Genome Engineering)

Requirements

The following are third-party software packages that must be installed on the system. Python requirements are described in the Installation section below.

Unafold (required for secondary structure calculation).

1. Download and install from here http://dinamelt.rit.albany.edu/download.php

• If using linux, you probably want to download the RPM and use these instructions: https://overlappingminds.com/sh/thoughts/0aa6d79e-fb8b-4f84-b287-f8e4494eac49

Installation

The setup.py config isn't ready yet, so please use the following installation procedure:

1. Install virtualenv if you don't have it yet. (You may want to install pip first.)

2. Create a new virtual environment for this project. This virtual environment isn't part of the project so just put it somewhere on your machine.

    $ virtualenv /path/to/venv/project-venv
   

   If you want to use a version of python different from the OS default you can specify the python binary with the '-p' option:

    $ virtualenv -p /usr/local/bin/python2.7 /path/to/venv/project-venv
   

3. Activate the environment in the shell. This will use python and other binaries like pip that are located your pyenv. You should do this whenever running any python/django scripts.

    $ source /path/to/venv/project-venv/bin/activate .
   

4. Install the dependencies in your virtual environment. We've exported the requirements in the requirements.txt file. In theory, these should all be installable with the single command:

    (venv)$ pip install -r requirements.txt
   

However, in reality, this doesn't seem to work perfectly. Specific issues:

• Manually install numpy using pip first.

    (venv)$ pip install numpy
  

Running Tests

With the correct python environment, run:

$ python setup.py test

If the above isn't working, you can use nose directly for testing from the top-level directory (one directory above the tests/ directory), by running (with the virtualenv enabled on the shell):

(venv)$ nosetests

Usage

There is currently a single script that does all the work: src/optmage/oligo_designer.py.

The user can list all the options available by running (remember to use the proper virtualenv):

(venv)$ python oligo_designer.py -h

By default the script creates oligos based on the configuration in src/optmage/data/INPUT_targets.txt, relative to the reference genome src/optmage/data/mg1655.fasta. Users should specify different inpus using the above flags.

NOTE: The script currently has defaults tuned to the canonical E. coli MG1655 strain so using a different strain may require some edits.