Usage

biopax2cabiom is a script to transform a BioPAX RDF data from a triplestore to a CADBIOM model.

usage: biopax2cabiom [-h] [-vv [VERBOSE]] {tests,model} ...

Named Arguments

-vv, --verbose Default: “info”

Sub-commands:

tests

Translates BioPAX test cases to cadbiom models and compares
them with the cadbiom model reference (if it exists).
biopax2cabiom tests [-h]

model

Make CADBIOM model with BioPAX data obtained from a triplestore.

biopax2cabiom model [-h]
                    (--getGraphUris | --listOfGraphUri LISTOFGRAPHURI [LISTOFGRAPHURI ...])
                    [--provenanceUri [PROVENANCEURI]]
                    [--triplestore [TRIPLESTORE]]
                    [--limit_sparql_results [LIMIT_SPARQL_RESULTS]]
                    [--pickleBackup] [--pickleDir [PICKLEDIR]]
                    [--cadbiomFile [CADBIOMFILE]] [--convertFullGraph]
                    [--fullCompartmentsNames] [--no_scc_fix]
                    [--blacklist [BLACKLIST]]

Named Arguments

--getGraphUris

Get the list of RDF and BioPAX graphs stored on the triplestore.

Default: False

--listOfGraphUri
 List of RDF graph to be queried on the triplestore.
--provenanceUri
 URI of the queried subgraph.
--triplestore

URL of the triplestore.

Default: “http://127.0.0.1:8890/sparql/

--limit_sparql_results
 

Limit the number of results for each SPARQL query.This allows to fine-tune the requests depending on the server being queried.

Default: 4000

--pickleBackup

Allows to save/reuse the results of SPARQL queries.The goal is to save querying time during tests with same inputs.

Default: False

--pickleDir

Output file path to save the script variables.

Default: “/tmp/backupPickle/backup.p”

--cadbiomFile

Output file path to generate the Cadbiom model.2 models are created: A basic model and a model without strongly connected components that block CADBIOM solver.

Default: “output/model.bcx”

--convertFullGraph
 

Converts all entities to cadbiom nodes, even the entities not used.

Default: False

--fullCompartmentsNames
 

If set, compartments will be encoded on the base of their real names instead of numeric values.

Default: False

--no_scc_fix

If set, strongly connected components will NOT be fixed in a second model file.

Default: False

--blacklist If set, the entities in the given file will bebanished from conditions of transitions (ex: cofactors or entities of energy metabolism)