README.md

minisana

Miniature Simulated Annealing Network Aligner

Install

Running make will do a few things:

1. compile object files in _objs
2. build the binary bin/mini
3. build the shared library lib/libmini.so
4. create empty directories output where .json files will be stored

Tests

Run tests with make test. Along with showing the test results, a coverage report will be generated as coverage/report.html. Open the report in your browser to see the total code coverage. make docker will also run the tests during image creation.

Docker

You can build a minisana image with make docker or go straight to running it with:

MINIOPTS="-n input/yeast.gw -N input/human.gw -t 10000000" make docker_run

Then you can check the logs with docker logs -f <container-id>. Once it's finished, you can check the json file written to ~/output.

Usage

./bin/mini -n,-N [-s,-a,-o,-t]

  -n: path to the smaller network
  -N: path to the bigger network (small n, big N... get it?)
  -s: path to sequence file [defaults to "input/yeast_human.bitscores"]
  -a: alpha value [defaults to 0.5]
  -o: file to output json [defaults to ./mini.out.json]
  -t: amount of time to run simulation [defaults to 100,000,000 iterations]

Example

make
./bin/mini -n input/yeast.gw -N input/human.gw
# or
./bin/mini -n input/yeast.gw -N input/human.gw -s input/yeast_human.bitscores
# or
./bin/mini -n input/yeast.gw -N input/human.gw -s input/yeast_human.bitscores -a 0.995
# or
./bin/mini -n input/yeast.gw -N input/human.gw -a 0.995

Planning

Check out our kanban board