update_clade

#!/usr/bin/env bash


# make clade table
# awk -F '\t' -v clade="clade"  '
# NR==1 {
#   for (i=1; i<=NF; i++){
#     ix[$i]=i
#   }
#   print "name","label","priority"}
# NR>1  {
#   if(!($ix[clade] in p)) {
#     print $ix[clade], $ix[clade], NR; p[$ix[clade]]=$ix[clade]
#   }
# }' OFS='\t' /tmp/dbDb2.tsv > /tmp/clade.tsv
echo "preparing clade"
awk -F '\t' '{
  if(NR==1){
    for (i=1; i<=NF; i++){cols[$i]=i}
    print "name","label","priority"
  }
  if(NR>1 && !seen[$cols["clade"]]){
    print $cols["clade"], $cols["clade"], NR
    seen[$cols["clade"]]++
  }
}' OFS='\t' /tmp/dbDb.tsv > /tmp/clade.tsv
hgsql -e "delete from hgcentral.clade"
hgsql -e "load data local infile \"/tmp/clade.tsv\" into table hgcentral.clade ignore 1 lines;"