From 97bc4dc77aced021d2c22d70b5aa304e86b6c8eb Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Wed, 14 Mar 2012 10:52:32 +0000
Subject: [PATCH] undetermined files get now the Flow Cell Name in the file
Name, otherwise these files are not unique
SVN: 24721
---
.../dist/etc/data-set-handler-unaligned.py | 15 ++++++++++++++-
1 file changed, 14 insertions(+), 1 deletion(-)
diff --git a/deep_sequencing_unit/dist/etc/data-set-handler-unaligned.py b/deep_sequencing_unit/dist/etc/data-set-handler-unaligned.py
index 860679da985..c47815e82b4 100755
--- a/deep_sequencing_unit/dist/etc/data-set-handler-unaligned.py
+++ b/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
--
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