6a1db42395f283de1421bd45e9d245ba2f896005
max
  Wed Dec 7 03:38:42 2022 -0800
commit panelApp otto changes, refs #30212

diff --git src/hg/utils/otto/panelApp/updatePanelApp src/hg/utils/otto/panelApp/updatePanelApp
index cf71149..a5c22b3 100755
--- src/hg/utils/otto/panelApp/updatePanelApp
+++ src/hg/utils/otto/panelApp/updatePanelApp
@@ -1,44 +1,44 @@
-#!/usr/bin/env python3
+#!/hive/data/outside/otto/panelApp/venv/bin/python3
 from datetime import date
 import os
 import shutil
 
 # the script uses relative pathnames, so make sure we're always in the right directory
 os.chdir("/hive/data/outside/otto/panelApp")
 
 # The code came in three files from Beagan with a lot of code duplication
 # One per subtrack
 # This is why it's still split over three separate Python files
 import genes
 import tandRep
 import cnv
 
 def getArchDir(db):
     " return hgwdev archive directory given db "
     dateStr = date.today().strftime("%Y-%m-%d")
     archDir = "/usr/local/apache/htdocs-hgdownload/goldenPath/archive/%s/panelApp/%s" % (db, dateStr)
     if not os.path.isdir(archDir):
         os.makedirs(archDir)
     return archDir
 
 def writeBb(hg19Table, hg38Table, subTrack):
     " sort the pandas tables, write to BED and convert "
     for db in ["hg19", "hg38"]:
         archDir = getArchDir(db)
 
-        bedFname = "current/%s/%s.bed.tmp" % (db, subTrack)
+        bedFname = "current/%s/%s.bed" % (db, subTrack)
         bbFname = "current/%s/%s.bb.tmp" % (db, subTrack)
 
         if db=="hg19":
             pdTable = hg19Table
         else:
             pdTable = hg38Table
 
         # for cnvs, one of the arguments can be None
         if pdTable is None:
             continue
 
         pdTable.sort_values(by=['chrom','chromStart'], ascending = (True, True), inplace=True)
         pdTable.to_csv(bedFname, sep='\t', index=False, header=None)
 
         asFname = subTrack+".as"