Genomics protos

This project contains protocol buffer definitions for working with genomics data. These definitions are based on the google.genomics.v1.* protos from googleapis, but with the API-specific pieces removed.

For convenience, this package also contains pre-compiled Python versions of the protobufs which can be installed using pip via the instructions below.

License

This code is licensed under the terms of the Apache license.

Disclaimer

• This is not an official Google product.

Installing for Python

You are welcome to use the .proto files directly. For Python specifically, we provide pre-compiled files that can be installed via pip.

Optional but recommended: start a virtualenv

$ cd
$ virtualenv my_genomics
$ source my_genomics/bin/activate

Now cd just above the genomics_protos directory and install:

pip install --upgrade genomics_protos/

You can now use the protos. For example:

$ python
from google.genomics.v1 import readalignment_pb2
r = readalignment_pb2.Read()
r.alignment.position.reference_name = 'chr1'
r.alignment.position.position = 1000000

How these files are generated

The *_pb2 files are generated as follows:

$ protoc google/genomics/v1/*.proto --python_out=.