da377fdc8a33c352274795c5817d8d117e03ae10
max
  Tue Oct 4 03:30:08 2022 -0700
more panelApp fixes, partially found by QA, refs #25568

diff --git src/hg/utils/otto/panelApp/updatePanelApp src/hg/utils/otto/panelApp/updatePanelApp
index 3e12fcb..cf71149 100755
--- src/hg/utils/otto/panelApp/updatePanelApp
+++ src/hg/utils/otto/panelApp/updatePanelApp
@@ -1,91 +1,93 @@
 #!/usr/bin/env 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)
         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"
 
         # -extraIndex=geneName 
         cmd = "bedToBigBed -tab -as=%s -type=bed9+26 %s /hive/data/genomes/%s/chrom.sizes %s" % (asFname, bedFname, db, bbFname)
         assert(os.system(cmd)==0)
 
         # put a copy into the archive
         archBbFname = archDir+"/%s.bb" % subTrack
         shutil.copyfile(bbFname, archBbFname)
 
 def updateGbdbSymlinks():
     " update the symlinks in /gbdb. Not really necessary but kept this code just in case. "
     for db in ["hg19", "hg38"]:
         archDir = getArchDir(db)
         for subTrack in ["genes", "tandRep", "cnv"]:
+            if subTrack=="cnv" and db=="hg19":
+                continue # no cnv on hg19
             cmd = "ln -sf `pwd`/current/%s/%s.bb /gbdb/%s/panelApp/%s.bb" % (db, subTrack, db, subTrack)
             assert(os.system(cmd)==0)
 
 def flipFiles():
     " rename the .tmp files to the final filenames "
     for db in ["hg19", "hg38"]:
         archDir = getArchDir(db)
         for subTrack in ["genes", "tandRep", "cnv"]:
             if db=="hg19" and subTrack=="cnv":
                 # no cnvs for hg19 yet
                 continue
             oldFname = "current/%s/%s.bb.tmp" % (db, subTrack)
             newFname = "current/%s/%s.bb" % (db, subTrack)
             os.replace(oldFname, newFname)
 
 def main():
     " create the 2 x three BED files and convert each to bigBed and update the archive "
     hg19Bed, hg38Bed = genes.downloadGenes()
     writeBb(hg19Bed, hg38Bed, "genes")
 
     hg19Bed, hg38Bed = tandRep.downloadTandReps()
     writeBb(hg19Bed, hg38Bed, "tandRep")
 
     hg38Bed = cnv.downloadCnvs()
     # no hg19 CNV data yet from PanelApp
     writeBb(None, hg38Bed, "cnv")
 
     flipFiles()
     updateGbdbSymlinks()
 
     print("PanelApp otto update: OK")
 
 main()