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Genome Engineering Tool

Project description

Edge keeps structural changes between a genome and child genomes derived from it. A user creates a modified genome by applying a sequence-based operation, such as homologous recombination, to a parent genome. Users can annotate or make corrections to sequences on a genome; Edge automatically applies the changes to the appropriate regions on the derived genomes. Edge does this efficiently: making a change on a parent genome takes O(1) and is automatically propagated to the modified genomes.

Edge uses O(D) amount of storage for each modified genome, where D is the number of differences between a modified genome and its parent. The current implementation additionally keeps a cache of annotations to base pair numbers, but this cache is soft-data and is invalidated and re-built on demand.

A modified genome can be re-created by re-applying operations to a new genome (think git rebase). Currently, however, annotating a genome is not an operation. Also, applying the same operation to a genome twice results in a single child genome, not two.

Edge provides UIs to look at operations and changes and APIs for making changes. Edge can export genome sequences and annotations as GFF files. While Edge comes with a simple UI for browsing features and sequences, the UI is primitive compared to other specialized applications.

Try it using Docker

make start-ext

Then check it out in your browser: http://localhost:9000/edge/#/genomes

Example: to import an genome, try

make add-s288c-ext

Or, if your app is already running, make add-s288c-ext_fast, which will run the job without trying to rebuild the image.

The Makefile holds all the commands necessary for managing the server and database, both in usage and development. Run make without arguments to see a list of commmands.

The Docker environment is defined in docker-compose.yml. Ese the edge service for your commands.

Of course, any of these make targets can be run directly from a shell inside a container from either service:

you@localhost:edge$ docker-compose run --rm edge bash
# Now you're inside the Docker container
root@docker-image:/usr/src/edge# make test

Try it without Docker

On your own machine, Construct your virtual environment and pip-install dependencies (use requirements.txt).

To start a server, first update src/server/ to use either sqlite or MySQL. For MySQL, create the appropriate databse. Then,

make migrate (cd example; gunzip ecoli-mg1655.gff.gz; gunzip yeast.gff.gz) python src/ import_gff ‘E. coli MG1655’ example/ecoli-mg1655.gff python src/ import_gff ‘Saccharomyces cerevisiae’ example/yeast.gff make run

Then set your browser to http://localhost:8000/edge/. Note the port is different than the Docker case

If you need NCBI BLAST or Primer3 support, you’ll need to make sure the packages are installed on your system. Debian and Ubuntu distributions provide binary versions of both of these packages.

Depending on where the NCBI BLAST tools and Primer3 are installed, you will probably need to tell edge where to find them, using the following environment variables:

NCBI_BIN_DIR       # Path to directory holding ncbi binaries, e.g. /usr/bin
PRIMER3_BIN        # Path to primer3 binary, e.g. /usr/bin/primer3_core
PRIMER3_CONFIG_DIR # Path to primer3 config directory, e.g. etc/primer3_config/

Then, to set up the edge BLAST db, from the src subdirectory,

python build_edge_blastdb

Editing data

You can edit genome and fragment metadata, such as name, notes, circular attributes, from the Django admin. Create a Django admin superuser, (see the superuser make target), then set your browser to the /admin/ endpoint of wherever you are running your dev server.

Deploying to production

Do not use the Dockerfile as-is for production, or the make run task. Django’s runserver command is not meant to run a production server. Instead, you’ll need to spin up a production WSGI server and run the Django projct with that, with your own settings. In this situation, it’s better to simply install the edge-genome python package on your deployed system and add it to your deployment Django server’s installed_apps setting.

Development, testing, and package release

When developing locally, you can run tests in the controlled environment of the docker container from your local machine with make test-ext.

Edge is versioned semantically. Continuous integration is done automatically on all branches through Travis CI, and tagged commits to master are automatically released to PyPI. To release a new version, bump the version number with the appropriate severity of the changes (major, minor, or patch), and push the resulting tagged commits to the GitHub remote repo:

you@localhost:edge$ make bump/patch-ext # Or bump/major, or bmp/minor
you@localhost:edge$ git push --tags origin master

If you cannot push to master directly, do the same thing on a new branch and submit a pull request.

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Filename, size & hash SHA256 hash help File type Python version Upload date
edge_genome-0.4.0-py2-none-any.whl (2.6 MB) Copy SHA256 hash SHA256 Wheel py2
edge-genome-0.4.0.tar.gz (2.4 MB) Copy SHA256 hash SHA256 Source None

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