d0aad7f66c2fee0fa9366c3b3caf4d761750c055
braney
  Tue Aug 17 10:27:07 2021 -0700
first version of Gencode genes (knownGene version) for mm39

diff --git src/hg/utils/otto/knownGene/buildKegg.sh src/hg/utils/otto/knownGene/buildKegg.sh
new file mode 100755
index 0000000..f1d3369
--- /dev/null
+++ src/hg/utils/otto/knownGene/buildKegg.sh
@@ -0,0 +1,35 @@
+#!/bin/sh -ex
+mkdir -p $dir/kegg
+cd $dir/kegg
+
+# Make the keggMapDesc table, which maps KEGG pathway IDs to descriptive names
+cp /cluster/data/hg19/bed/ucsc.14.3/kegg/map_title.tab .
+# wget --timestamping ftp://ftp.genome.jp/pub/kegg/pathway/map_title.tab
+cat map_title.tab | sed -e 's/\t/\thsa\t/' > j.tmp
+cut -f 2 j.tmp >j.hsa
+cut -f 1,3 j.tmp >j.1
+paste j.hsa j.1 |sed -e 's/\t//' > keggMapDesc.tab
+rm j.hsa j.1 j.tmp
+hgLoadSqlTab -notOnServer $tempDb keggMapDesc $kent/src/hg/lib/keggMapDesc.sql keggMapDesc.tab
+
+# Following in two-step process, build/load a table that maps UCSC Gene IDs
+# to LocusLink IDs and to KEGG pathways.  First, make a table that maps 
+# LocusLink IDs to KEGG pathways from the downloaded data.  Store it temporarily
+# in the keggPathway table, overloading the schema.
+cp /cluster/data/hg19/bed/ucsc.14.3/kegg/hsa_pathway.list .
+
+cat hsa_pathway.list| sed -e 's/path://'|sed -e 's/:/\t/' > j.tmp
+hgLoadSqlTab -notOnServer $tempDb keggPathway $kent/src/hg/lib/keggPathway.sql j.tmp
+
+# Next, use the temporary contents of the keggPathway table to join with
+# knownToLocusLink, creating the real content of the keggPathway table.
+# Load this data, erasing the old temporary content
+hgsql $tempDb -B -N -e 'select distinct name, locusID, mapID from keggPathway p, knownToLocusLink l where p.locusID=l.value' > keggPathway.tab
+hgLoadSqlTab -notOnServer $tempDb \
+    keggPathway $kent/src/hg/lib/keggPathway.sql  keggPathway.tab
+
+# Finally, update the knownToKeggEntrez table from the keggPathway table.
+hgsql $tempDb -B -N -e 'select kgId, mapID, mapID, "+", locusID from keggPathway' |sort -u| sed -e 's/\t+\t/+/' > knownToKeggEntrez.tab
+hgLoadSqlTab -notOnServer $tempDb knownToKeggEntrez $kent/src/hg/lib/knownToKeggEntrez.sql knownToKeggEntrez.tab
+
+echo "BuildKegg successfully finished"