diff --git a/work/export.sh b/work/export.sh index 1d828142..a1efaabb 100755 --- a/work/export.sh +++ b/work/export.sh @@ -7,15 +7,14 @@ $JAVA_HOME/bin/java -Xmx64g -Dpaxtools.CollectionProvider=org.biopax.paxtools.tr $JAVA_HOME/bin/java -Xmx64g -Dpaxtools.CollectionProvider=org.biopax.paxtools.trove.TProvider -Dpaxtools.normalizer.use-latest-registry=true -Dpaxtools.core.use-latest-genenames=true -jar paxtools.jar toSIF 'pc-biopax.owl.gz' 'pc-hgnc.txt' seqDb=hgnc -extended -andSif exclude=neighbor_of -rename 's/txt\.sif/sif/' *.txt.sif -gzip *.txt *.sif *.gmt - $JAVA_HOME/bin/java -Xmx64g -Dpaxtools.CollectionProvider=org.biopax.paxtools.trove.TProvider -Dpaxtools.normalizer.use-latest-registry=true -Dpaxtools.core.use-latest-genenames=true -jar paxtools.jar summarize 'pc-biopax.owl.gz' 'pathways.txt' --pathways $JAVA_HOME/bin/java -Xmx64g -Dpaxtools.CollectionProvider=org.biopax.paxtools.trove.TProvider -Dpaxtools.normalizer.use-latest-registry=true -Dpaxtools.core.use-latest-genenames=true -jar paxtools.jar summarize 'pc-biopax.owl.gz' 'physical_entities.json' --uri-ids cat physical_entities.json | jq -cS 'map(select(.generic)) | reduce .[] as $o ({}; . + {($o.uri): {name: $o.name, label:$o.label, synonyms:$o."hgnc.symbol"}})' > generic-physical-entity-map.json -gzip pathways.txt physical_entities.json + +rename 's/txt\.sif/sif/' *.txt.sif +gzip *.txt *.sif *.gmt physical_entities.json cd .. -echo "export.sh completed." +echo "export.sh completed." \ No newline at end of file