3b0d251fc556419285eca98739c70f717a9ac9b7
braney
  Sat Oct 17 06:31:52 2020 -0700
add Max's OMIM bigify scripts to tree

diff --git src/hg/utils/otto/omim/bigifyOmim.sh src/hg/utils/otto/omim/bigifyOmim.sh
new file mode 100644
index 0000000..7a602aa
--- /dev/null
+++ src/hg/utils/otto/omim/bigifyOmim.sh
@@ -0,0 +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 $db -NB -e 'select chrom, chromStart, chromEnd, name, "0", ".", chromStart, chromEnd, "color", geneSymbol, "", "" from omimGene2 JOIN omimGeneMap ON omimGene2.name=omimGeneMap.omimId LEFT OUTER JOIN omimPhenotype on omimGene2.name=omimPhenotype.omimId where phenotypeId is NULL' >> omimGene2.tmp
+bedSort omimGene2.tmp omimGene2.tmp
+python omimGene2ToBigBed.py omimGene2.tmp /hive/data/genomes/$db/chrom.sizes 2020-06-22/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 
+done