30e9677ddc4349e1f54dec3d406d7c229502c2ae
lrnassar
  Tue Nov 16 16:09:06 2021 -0800
Fixing up discrepancies between hive and tree for otto, refs #28331

diff --git src/hg/utils/otto/omim/bigifyOmim.sh src/hg/utils/otto/omim/bigifyOmim.sh
index 7a602aa..440c8d6 100644
--- src/hg/utils/otto/omim/bigifyOmim.sh
+++ src/hg/utils/otto/omim/bigifyOmim.sh
@@ -1,22 +1,22 @@
 #omimGenemap2ToInhTable 2020-05-18/genemap2.txt 2020-05-18/hg38/genemap2inheritance.tab
 #doOmimPhenotypeInherit 2020-05-18/genemap2.txt 2020-05-18/hg38/omimPhenotype2.tab 
 #hgLoadSqlTab -verbose=0 -warn hg38 omimPhenotypeNew ~/kent/src/hg/lib/omimPhenotype.sql 2020-05-18/hg38/omimPhenotype2.tab
 #hgLoadSqlTab -verbose=0 -warn hg38 omimPhenotype ~/kent/src/hg/lib/omimPhenotype.sql 2020-05-18/hg38/omimPhenotype2.tab
 #hgsql hg19 -e 'select chrom, chromStart, chromEnd, name, "0", ".", chromStart, chromEnd, "color", geneSymbol, disorders1, GROUP_CONCAT(omimPhenotype.description, "|", omimPhenoMapKey, "|", inhMode SEPARATOR "$") from omimGene2, omimGeneMap, omimPhen
 #otype where omimGene2.name=omimGeneMap.omimId and omimGene2.name=omimPhenotype.omimId'
 #python fixupBed.py  > omimGene2bb.bed
 #bedToBigBed omimGene2bb.bed /hive/data/genomes/hg19/chrom.sizes omimGene2bb.bb -tab -as=omimGene2.as -type=bed9+
 #bedToBigBed omimGene2bb.bed /hive/data/genomes/hg19/chrom.sizes omimGene2.bb -tab -as=omimGene2.as -type=bed9+
 #bedSort omimGene2bb.bed omimGene2bb.bed
 #bedToBigBed omimGene2bb.bed /hive/data/genomes/hg19/chrom.sizes omimGene2.bb -tab -as=omimGene2.as -type=bed9+
 
 set -e
 for db in hg19 hg38; do
-hgsql $db -e 'select chrom, chromStart, chromEnd, name, "0", ".", chromStart, chromEnd, "color", geneSymbol, disorders1, GROUP_CONCAT(omimPhenotype.description, "|", omimPhenoMapKey, "|", inhMode SEPARATOR "$") from omimGene2, omimGeneMap, omimPhenotype where omimGene2.name=omimGeneMap.omimId and omimGene2.name=omimPhenotype.omimId GROUP BY chrom, chromStart, chromEnd, omimGeneMap.omimId ' -NB  > omimGene2.tmp
-hgsql $db -NB -e 'select chrom, chromStart, chromEnd, name, "0", ".", chromStart, chromEnd, "color", geneSymbol, "", "" from omimGene2 JOIN omimGeneMap ON omimGene2.name=omimGeneMap.omimId LEFT OUTER JOIN omimPhenotype on omimGene2.name=omimPhenotype.omimId where phenotypeId is NULL' >> omimGene2.tmp
+hgsql $db -e 'select chrom, chromStart, chromEnd, name, "0", ".", chromStart, chromEnd, "color", geneSymbol, disorders1, GROUP_CONCAT(omimPhenotype.description, "|", omimPhenoMapKey, "|", inhMode SEPARATOR "$"), omimPhenoMapKey from omimGene2, omimGeneMap, omimPhenotype where omimGene2.name=omimGeneMap.omimId and omimGene2.name=omimPhenotype.omimId GROUP BY chrom, chromStart, chromEnd, omimGeneMap.omimId ' -NB  > omimGene2.tmp
+hgsql $db -NB -e 'select chrom, chromStart, chromEnd, name, "0", ".", chromStart, chromEnd, "color", geneSymbol, "", "", "0" from omimGene2 JOIN omimGeneMap ON omimGene2.name=omimGeneMap.omimId LEFT OUTER JOIN omimPhenotype on omimGene2.name=omimPhenotype.omimId where phenotypeId is NULL' >> omimGene2.tmp
 bedSort omimGene2.tmp omimGene2.tmp
-python omimGene2ToBigBed.py omimGene2.tmp /hive/data/genomes/$db/chrom.sizes 2020-06-22/omimGene2.$db.bb 
+python omimGene2ToBigBed.py omimGene2.tmp /hive/data/genomes/$db/chrom.sizes 2020-10-22/omimGene2.$db.bb 
 #rm omimGene2.tmp 
 rm -f /gbdb/$db/bbi/omimGene2.bb
-ln -s `pwd`/2020-06-22/omimGene2.$db.bb /gbdb/$db/bbi/omimGene2.bb 
+ln -s `pwd`/2020-10-22/omimGene2.$db.bb /gbdb/$db/bbi/omimGene2.bb 
 done