25e67bf9ad9092811cb1879591f736b4373c5da9
gperez2
  Thu Jul 14 16:37:02 2022 -0700
Updating script to accommodate hg38/mm39 pushedout tables for hgw1, no RM

diff --git src/utils/qa/checkSyncAndMetaDataAll.py src/utils/qa/checkSyncAndMetaDataAll.py
index c8c75b9..04db881 100755
--- src/utils/qa/checkSyncAndMetaDataAll.py
+++ src/utils/qa/checkSyncAndMetaDataAll.py
@@ -1,37 +1,40 @@
 #Lou - 14/08/19
 
 #Make a list of all assemblies in hgCentral with active=1
 allDbs = get_ipython().getoutput(u'hgsql -h genome-centdb -e "SELECT name FROM dbDb WHERE active = 1 ORDER BY RAND()" hgcentral | grep -v "name"')
 
 #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 == '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):
+            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 '  0 hgw1.only' not in str(checkSyncResults) and '  3 hgwbeta.only' not in str(checkSyncResults):
+        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 == '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)