All of the BEL scripts in the current working directory (and sub-directories) can be pickled in-place with the following command (add -d
to specify a different directory)
$ pybel-tools io convert -d ~/bms/aetionomy/
Before running the service, some data can be pre-loaded in your cache.
The Selventa Small Corpus and Large Corpus are two example BEL documents distributed by the OpenBEL framework. They are good examples of many types of BEL statements and can be used immediately to begin exploring. Add -v
for more logging information during compilation. This is highly suggested for the first run, since it takes a while to cache all of the namespaces and annotations. This only has to be done once, and will be much faster the second time!
$ pybel-tools ensure small_corpus -v
$ pybel-tools ensure large_corpus -v
$ pybel-tools ensure gene_families -v
$ pybel-tools ensure named_complexes -v
A single network stored as a PyBEL gpickle can quickly be uploaded using the following code:
$ pybel-tools io upload -p /path/to/my_network.gpickle
Multiple networks in a given directory and sub-directories can be uploaded by adding the -r
tag.
$ pybel-tools io upload -p ~/bms/aetionomy/ -r