ad9d2ac60828bebace74450afabb7557410a7fbc
max
  Mon Jan 23 12:07:24 2023 -0800
adding rs prefix to dbSnp ids in clinvar otto job, no redmine, email from Bob

diff --git src/hg/utils/otto/clinvar/clinVarToBed src/hg/utils/otto/clinvar/clinVarToBed
index a624c3d..7fe96d2 100755
--- src/hg/utils/otto/clinvar/clinVarToBed
+++ src/hg/utils/otto/clinvar/clinVarToBed
@@ -865,35 +865,39 @@
         name = name[:90]+"..."
     name = varId+"|"+name
 
     if len(mouseOverName)>80:
         mouseOverName = mouseOverName[:80]+"..."
 
     #if len(hgvsProt) > 90:
         #hgvsProt = hgvsProt[:90]+"..."
     #if len(hgvsCod) > 90:
         #hgvsCod = hgvsCod[:90]+"..."
 
     phenotypeIds, _ = accListToHtml(phenotypeIds)
 
     starRatingHtml, asciiStars, starCount = reviewStatusToHtmlStars(reviewStatus)
 
+    phenotypeList = ", ".join(phenotypeList.split("|"))
+
     mouseOverParts = [mouseOverName, "Type: "+allType, "Consequence: "+ molConseq, "Significance: "+clinSign,
             "Origin: "+origin, "Phenotypes: "+phenotypeList]
     # removed Apr 2020: numberSubmitters+" submitters", "Level: "+asciiStars
     mouseOver = ", ".join(mouseOverParts)
 
+    snpAcc = "rs"+snpAcc # dbSnp links changed in mid/late 2022
+
     row = [chrom, start, end, shortName, str(starCount), strand, thickStart, thickEnd, itemRgb, \
         blockCount, blockSizes, blockStarts,
         name, clinSign, starRatingHtml, allType, geneStr, molConseq,
         snpAcc, dbVarAcc, irvcAcc, inGtr, phenotypeList, phenotypeIds, origin, assembly, cytogenetic,
         hgvsTable, "", numberSubmitters, lastEval, guidelines, otherIds, mouseOver,
         # these fields are the for the filters, not for the display
         pathoCode, originCode, allTypeCode, str(varLen), str(starCount),
         # the variant ID got forgotten in the original bigBed schema, it was only part of the origName field
         varId, dbVarSsvAcc]
 
     # replace clinvar's placeholders with real empty fields
     newRow = []
     for x in row:
         if x in ["-1", "-"]:
             newRow.append("")