undetermined files get now the Flow Cell Name in the file Name, otherwise...

undetermined files get now the Flow Cell Name in the file Name, otherwise these files are not unique

SVN: 24721

deep_sequencing_unit/dist/etc/data-set-handler-unaligned.py

@@ -10,7 +10,7 @@ import os
 import glob
 import shutil
 import time
-from java.lang import RuntimeException
+#from java.lang import RuntimeException
 from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
 from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchSubCriteria
 
@@ -30,6 +30,14 @@ def touch_markerfile(filename):
   except:
     print('Could not touch ' + filename)  
 
+def renameFiles(dir, flowcellName):
+  print dir 
+  print flowcellName
+  for root, dirs, files in os.walk(dir):
+    for file in files:
+      print root + file
+      os.rename(root + '/' + file, root + "/" + flowcellName + "_" + file)
+
 
 # Create a "transaction" -- a way of grouping operations together so they all
 # happen or none of them do.
@@ -56,6 +64,10 @@ laneList.sort()
 
 undeterminedList=glob.glob(incomingPath + '/'+ UNALIGNED_FOLDER + REGEX_UNDETERMINED)
 undeterminedList.sort()
+
+# add the Flow Cell Name to the Undetermined FASTQ files
+[renameFiles(dir, flowcell) for dir in undeterminedList]
+
 # Multiplexing:
 # First move the Undetermined reads to the other ones 
 [shutil.move(undeterminedLane, laneList[int(undeterminedLane.split('/')[-1][-1])-1] +'/' + undeterminedLane.split('/')[-1]) for undeterminedLane in undeterminedList]
@@ -76,6 +88,7 @@ transaction.createNewDirectory(dataSet, UNALIGNED_FOLDER)
 # move all files is data set
 [transaction.moveFile(file, dataSet, UNALIGNED_FOLDER)  for file in fileList]
 # move base call stat dir into data set
+print("flowcell: "+flowcell)
 transaction.moveFile(incomingPath + '/' + UNALIGNED_FOLDER + '/' +  BASECALL_STATS_FOLDER + flowcell, dataSet, UNALIGNED_FOLDER + '/')
   
 # Get the search service