Usage¶
biopax2cabiom is a script to transform BioPAX RDF data from a triplestore to a CADBIOM model.
usage: biopax2cabiom [-h] [-vv [VERBOSE]] {tests,model,remove_scc} ...
Named Arguments¶
| -vv, --verbose | Default: “info” |
Sub-commands:¶
tests¶
- Run unit tests. Translate BioPAX test cases to Cadbiom models and
- compare them to the reference models.
biopax2cabiom tests [-h]
model¶
Build a Cadbiom model based on the BioPAX data obtained from a triplestore.
biopax2cabiom model [-h]
(--get_graph_uris | --graph_uris GRAPH_URIS [GRAPH_URIS ...])
[--provenance_uri [PROVENANCE_URI]]
[--triplestore [TRIPLESTORE]] [--limit [LIMIT]]
[--backup_queries] [--backup_file [BACKUP_FILE]]
[--cadbiom_model [CADBIOM_MODEL]] [--full_graph]
[--numeric_compartments] [--no_scc_fix]
[--blacklist_file [BLACKLIST_FILE]] [--show_metrics]
Triplestore options¶
| --get_graph_uris | |
Get the list of RDF and BioPAX graphs stored on the triplestore. Default: False | |
| --graph_uris | List of RDF graphs to be queried on the triplestore. |
| --provenance_uri | |
| URI of the queried subgraphs. | |
| --triplestore | Address (URL) of the triplestore endpoint. Default: “http://127.0.0.1:8890/sparql/” |
| --limit | Limit the size of data chuncks retrieved by a SPARQL query. This makes it possible to fine-tune the requests according to the configuration of the server queried. Default: 4000 |
Backup options¶
| --backup_queries | |
Allow to save and reload the results of SPARQL queries without re-interrogating the server. The goal is to save time and bandwidth on requests as long as the server data does not change. Default: False | |
| --backup_file | Backup file to save and reload the results of SPARQL queries. Default: “backup.p” |
Cadbiom model options¶
| --cadbiom_model | |
Filepath of the created Cadbiom model.Two models are created by default: A default model, and a model without Strongly Connected Components. See –no_scc_fix. Default: “output/model.bcx” | |
| --full_graph | Convert all entities to Cadbiom nodes, even the members of classes that aren’ involved in reactions. Default: False |
| --numeric_compartments | |
If set, compartment names will be based on numeric values instead of their real names. Default: False | |
| --no_scc_fix | If set, strongly connected components will NOT be fixed in asecond model. Default: False |
| --blacklist_file | |
| File which provides uris of entities that will be removed from the model (use it to eliminate cofactors or entities from energy metabolism for example). | |
| --show_metrics | Provide a summary about the data ready to be used to design a model. Default: False |