Command Line Interface¶
Pickling lots of BEL scripts¶
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/
Getting Data in to the Cache¶
Before running the service, some data can be pre-loaded in your cache.
Loading Selventa Corpra¶
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!
Small Corpus¶
$ pybel-tools ensure small_corpus -v
Large Corpus¶
$ pybel-tools ensure large_corpus -v
Loading Other Resources¶
Gene Families¶
$ pybel-tools ensure gene_families -v
Named Protein Complexes¶
$ pybel-tools ensure named_complexes -v
Uploading Precompiled BEL¶
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
Uploading Multiple Networks¶
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