aa8d3802ce419bcc4b5a0d40ec267ed77c047756
gperez2
  Wed Oct 16 09:26:06 2024 -0700
Updating script to accommodate mm39 relatedTrack_publict table for hgw1, no RM

diff --git src/utils/qa/checkSyncAndMetaDataAll.py src/utils/qa/checkSyncAndMetaDataAll.py
index cf2258f..19e4f85 100755
--- src/utils/qa/checkSyncAndMetaDataAll.py
+++ src/utils/qa/checkSyncAndMetaDataAll.py
@@ -5,56 +5,62 @@
 
 curatedHubs=['hs1','mpxvRivers']
 
 #Initialize list to hold assemblies with errors
 troubleDbs = []
 
 #Iterate through allDbs and run checkSync.csh comparing to hgw1
 for db in allDbs:
     checkSyncResults = get_ipython().getoutput(u"checkSync.csh '$db' hgw1 hgwbeta")
     if db in curatedHubs:
         continue
     if db == 'mm9':
         if '  0 hgw1.only' not in str(checkSyncResults) and '  4 hgwbeta.only' not in str(checkSyncResults):
             troubleDbs.append(db)
     elif db == 'mm39':
-        if '  2 hgw1.only' not in str(checkSyncResults) and '  2 hgwbeta.only' not in str(checkSyncResults):
+        if '  1 hgw1.only' not in str(checkSyncResults) and '  3 hgwbeta.only' not in str(checkSyncResults):
             troubleDbs.append(db)
     elif db == 'hg18':
         if '  0 hgw1.only' not in str(checkSyncResults) and '  4 hgwbeta.only' not in str(checkSyncResults):
             troubleDbs.append(db)
     elif db == 'hg19':
         if '  0 hgw1.only' not in str(checkSyncResults) and '  5 hgwbeta.only' not in str(checkSyncResults):
             troubleDbs.append(db)
     elif db == 'hg38':
         if '  3 hgw1.only' not in str(checkSyncResults) and '  3 hgwbeta.only' not in str(checkSyncResults):
             troubleDbs.append(db)
     else:
         if '  0 hgw1.only' not in str(checkSyncResults) and '  2 hgwbeta.only' not in str(checkSyncResults):
             troubleDbs.append(db)
     
 #Iterate through allDbs and run checkSync.csh comparing to hgw2, informing of discrepancies
 for db in allDbs:
     checkSyncResults = get_ipython().getoutput(u"checkSync.csh '$db' hgw2 hgwbeta")
     if db in curatedHubs:
         continue
     if db == 'mm9':
         if '  0 hgw1.only' not in str(checkSyncResults) and '  4 hgwbeta.only' not in str(checkSyncResults)             and db not in troubleDbs:
             get_ipython().system(u" echo There looks to be a discrepancy between hgw1 and hgw2 checkSync for: '$db'")
             get_ipython().system(u" echo Follow up with checkSync.csh '$db' hgw1 hgw2")
             get_ipython().system(u' echo')
             troubleDbs.append(db)
+    elif db == 'mm39':
+        if '  1 hgw1.only' not in str(checkSyncResults) and '  3 hgwbeta.only' not in str(checkSyncResults)             and db not in troubleDbs:
+            get_ipython().system(u" echo There looks to be a discrepancy between hgw1 and hgw2 checkSync for: '$db'")
+            get_ipython().system(u" echo Follow up with checkSync.csh '$db' hgw1 hgw2")
+            get_ipython().system(u' echo')
+            troubleDbs.append(db)
     elif db == 'hg18':
         if '  0 hgw1.only' not in str(checkSyncResults) and '  4 hgwbeta.only' not in str(checkSyncResults)             and db not in troubleDbs:
             get_ipython().system(u" echo There looks to be a discrepancy between hgw1 and hgw2 checkSync for: '$db'")
             get_ipython().system(u" echo Follow up with checkSync.csh '$db' hgw1 hgw2")
             get_ipython().system(u' echo')
             troubleDbs.append(db)
     elif db == 'hg19':
         if '  0 hgw1.only' not in str(checkSyncResults) and '  5 hgwbeta.only' not in str(checkSyncResults)             and db not in troubleDbs:
             get_ipython().system(u" echo There looks to be a discrepancy between hgw1 and hgw2 checkSync for: '$db'")
             get_ipython().system(u" echo Follow up with checkSync.csh '$db' hgw1 hgw2")
             get_ipython().system(u' echo')
             troubleDbs.append(db)
     elif db == 'hg38':
         if '  0 hgw1.only' not in str(checkSyncResults) and '  3 hgwbeta.only' not in str(checkSyncResults)             and db not in troubleDbs:
             get_ipython().system(u" echo There looks to be a discrepancy between hgw1 and hgw2 checkSync for: '$db'")