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[sallou]

Usage

Insert nodes

Loads an OBO file

java -classpath crawlogy-0.1-SNAPSHOT-jar-with-dependencies.jar:. -Xmx2048M org.irisa.genouest.ontology.App -db danaides -obo $1

Load a GFF file, replace -obo by -gff...

The batch option uses the Neo4J batch inserter. It manages differently the commits etc.. for a high number of inserts in a local mode (does not access a remote server but directly the files). This is preferred mode for DB setup.

A useRAM option can be disabled (default=true) to keep references in RAM during a file treatment to avoid too many DB requests. In case of out of memory issue with very large files ( or low performance computer), one can try to disable this option to reduce memory usage during inserts.

Search nodes

Extract nodes with descendant of "ontology" node, with upstream filter node "filter" (optional).
Limit results to max, data depth(ddepth) and filter depth (fdepth).
Depth restrict to 1 level (or no limit) the number of branch we should follow to get a match.
Host is where the Neo4J server is running to query it.
Datahost is the URL to query to extract the fasta content of a data node.

java -cp crawlogy-0.1-SNAPSHOT-jar-with-dependencies.jar org.irisa.genouest.ontology.Search -datahost "http://seqcrawler.genouest.org/cgi-bin/mongo/mongo.pl" -db /home/symbiose/osallou/neo/data -ontology 999 -host myhost:7474 -max 1000 -filter 12 -ddepth 1 -fdepth 1 -out myfile.fasta