d8fcb8618a0aed962c050c0914131e618304ced9
hiram
  Tue Feb 3 14:51:24 2026 -0800
preparing to add the haplotypes column to the table refs #34736

diff --git src/hg/hubApi/assemblyList.py src/hg/hubApi/assemblyList.py
index 9ed83080b07..a21a063783b 100755
--- src/hg/hubApi/assemblyList.py
+++ src/hg/hubApi/assemblyList.py
@@ -859,85 +859,85 @@
         if "na" not in gcAccession:
             if gcAccession in allStatus:
               stat = allStatus[gcAccession]
               refSeqCategory = stat['refSeqCategory'].lower()
               versionStatus = stat['versionStatus'].lower()
               assemblyLevel = stat['assemblyLevel'].lower()
             if gcAccession not in description:
               description += " " + gcAccession
         ### add alias names to description if they are not already there
         description = addAliases(dbDbName, aliasData, description)
 
         descr = f"{entry['sourceName']} {entry['taxId']} {description}"
         if year not in organism and year not in descr:
             descr = f"{entry['sourceName']} {entry['taxId']} {entry['description']} {year}"
         description = re.sub(r'\s+', ' ', descr).strip()
-        outLine =f"{entry['name']}\t{priority}\t{organism}\t{entry['scientificName']}\t{entry['taxId']}\t{clade}\t{description}\t1\t\t{year}\t{refSeqCategory}\t{versionStatus}\t{assemblyLevel}\n"
+        outLine =f"{entry['name']}\t{priority}\t{organism}\t{entry['scientificName']}\t{entry['taxId']}\t{clade}\t{description}\t1\t\t{year}\t{refSeqCategory}\t{versionStatus}\t{assemblyLevel}\t\n"
         fileOut.write(outLine)
         itemCount += 1
 
     totalItemCount += itemCount
     print(f"{totalItemCount:4} - total\tdbDb count: {itemCount:4}")
 
     itemCount = 0
     # Print the GenArk data
     for entry in genArkItems:
         gcAccession = entry['gcAccession']
         if gcAccession in allPriorities:
             priority = allPriorities[gcAccession]
         else:
             print("no priority for ", gcAccession)
             sys.exit(255)
 
         hubPath = genarkPath(gcAccession)
         commonName = entry['commonName']
         clade = entry['clade']
         year = entry['year']
         descr = f"{entry['asmName']} {entry['taxId']}"
         if year not in commonName and year not in descr:
             descr = f"{entry['asmName']} {entry['taxId']} {year}"
         ### add alias names to description if they are not already there
         descr = addAliases(gcAccession, aliasData, descr)
         description = re.sub(r'\s+', ' ', descr).strip()
         refSeqCategory = entry['refSeqCategory'].lower()
         versionStatus = entry['versionStatus'].lower()
         assemblyLevel = entry['assemblyLevel'].lower()
-        outLine = f"{entry['gcAccession']}\t{priority}\t{commonName.encode('ascii', 'ignore').decode('ascii')}\t{entry['scientificName']}\t{entry['taxId']}\t{clade}\t{description}\t1\t{hubPath}\t{year}\t{refSeqCategory}\t{versionStatus}\t{assemblyLevel}\n"
+        outLine = f"{entry['gcAccession']}\t{priority}\t{commonName.encode('ascii', 'ignore').decode('ascii')}\t{entry['scientificName']}\t{entry['taxId']}\t{clade}\t{description}\t1\t{hubPath}\t{year}\t{refSeqCategory}\t{versionStatus}\t{assemblyLevel}\t\n"
         fileOut.write(outLine)
         itemCount += 1
 
     totalItemCount += itemCount
     print(f"{totalItemCount:4} - total\tgenArk count: {itemCount:4}")
 
     incrementPriority = len(allPriorities) + 1
     print("# incrementing priorities from: ", incrementPriority)
 
     itemCount = 0
     # Print the refSeq/genBank data
     for entry in refSeqGenBankSorted:
         gcAccession = entry['gcAccession']
         commonName = entry['commonName']
         scientificName = entry['scientificName']
         asmName = entry['asmName']
         clade = entry['clade']
         year = entry['year']
         refSeqCategory = entry['refSeqCategory'].lower()
         versionStatus = entry['versionStatus'].lower()
         assemblyLevel = entry['assemblyLevel'].lower()
         descr = f"{asmName} {entry['taxId']} {entry['other']}"
         if year not in commonName and year not in descr:
             descr = f"{asmName} {entry['taxId']} {entry['other']} {year}"
         ### add alias names to description if they are not already there
         descr = addAliases(gcAccession, aliasData, descr)
         description = re.sub(r'\s+', ' ', descr).strip()
-        outLine = f"{gcAccession}\t{incrementPriority}\t{entry['commonName'].encode('ascii', 'ignore').decode('ascii')}\t{entry['scientificName']}\t{entry['taxId']}\t{clade}\t{description.encode('ascii', 'ignore').decode('ascii')}\t0\t\t{year}\t{refSeqCategory}\t{versionStatus}\t{assemblyLevel}\n"
+        outLine = f"{gcAccession}\t{incrementPriority}\t{entry['commonName'].encode('ascii', 'ignore').decode('ascii')}\t{entry['scientificName']}\t{entry['taxId']}\t{clade}\t{description.encode('ascii', 'ignore').decode('ascii')}\t0\t\t{year}\t{refSeqCategory}\t{versionStatus}\t{assemblyLevel}\t\n"
         fileOut.write(outLine)
         incrementPriority += 1
         itemCount += 1
 
     totalItemCount += itemCount
     print(f"{totalItemCount:4} - total\trefSeq + genbank count: {itemCount:4}")
 
     fileOut.close()
 
 if __name__ == "__main__":
     main()