From 602913e9aea4c74eef1b2f9cbc9ea7f59eae03e1 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Tue, 27 Sep 2011 08:30:31 +0000
Subject: [PATCH] fix the handling of multiplexed lanes with undetermined reads
SVN: 23092
---
.../dist/etc/data-set-handler-unaligned.py | 14 +++++++++-----
1 file changed, 9 insertions(+), 5 deletions(-)
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 3f0bd1e68a6..860679da985 100755
--- a/deep_sequencing_unit/dist/etc/data-set-handler-unaligned.py
+++ b/deep_sequencing_unit/dist/etc/data-set-handler-unaligned.py
@@ -18,7 +18,7 @@ BASECALL_STATS_FOLDER = 'Basecall_Stats_'
REGEX_FILES = '*.*'
REGEX_MAKEFILE = 'Make*'
REGEX_LANES='/P*'
-REGEX_UNDETERMINED = 'U*/Sample*'
+REGEX_UNDETERMINED = '/U*/Sample*'
UNALIGNED_FOLDER='Unaligned_no_mismatch'
LANE_FOLDER='/links/shared/dsu-dss/dss/incoming-jython-lanes/'
MARKER_STRING='.MARKER_is_finished_'
@@ -48,15 +48,19 @@ if (len(split) ==2):
flowcell=name.split("_")[-1]
# fix Illumina Script error: the GA FC Name does not contain a suffix A or B so noes not need to be removed
# but Illumina removes it anyway, so we just revert this
- os.rename(incomingPath + '/' + UNALIGNED_FOLDER + '/' + BASECALL_STATS_FOLDER + name.split("_")[-1][1:], incomingPath + '/' + UNALIGNED_FOLDER +'/' + BASECALL_STATS_FOLDER + flowcell)
+ #os.rename(incomingPath + '/' + UNALIGNED_FOLDER + '/' + BASECALL_STATS_FOLDER + name.split("_")[-1][1:], incomingPath + '/' + UNALIGNED_FOLDER +'/' + BASECALL_STATS_FOLDER + flowcell)
#move Lanes into a different drop box
-#print(incomingPath + '/'+ UNALIGNED_FOLDER + REGEX_LANES)
laneList=glob.glob(incomingPath + '/'+ UNALIGNED_FOLDER + REGEX_LANES)
laneList.sort()
-[shutil.move(lane, LANE_FOLDER+lane.split('/')[-1]) for lane in laneList]
+
undeterminedList=glob.glob(incomingPath + '/'+ UNALIGNED_FOLDER + REGEX_UNDETERMINED)
-[shutil.move(undeterminedLane, LANE_FOLDER+laneList[undeterminedLane.split('/')[-1][-1]]) for undeterminedLane in undeterminedList]
+undeterminedList.sort()
+# 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]
+
+[shutil.move(lane, LANE_FOLDER+lane.split('/')[-1]) for lane in laneList]
markerFileList = [touch_markerfile(LANE_FOLDER+MARKER_STRING+lane.split('/')[-1]) for lane in laneList]
# Create a data set and set type
--
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