From 67a4cf348810401da704cdaba376fd756f6e05a1 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Mon, 3 Apr 2017 14:45:04 +0000
Subject: [PATCH] -added support for 10x samples
SVN: 38008
---
.../Jython/createSampleSheet_bcl2fastq.py | 36 +++++++++++++++----
1 file changed, 29 insertions(+), 7 deletions(-)
diff --git a/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py b/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py
index 774f9a843dd..a465bcf8300 100644
--- a/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py
+++ b/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py
@@ -197,6 +197,8 @@ def readConfig(logger):
config_dict['externalSampleName'] = configParameters.get(OPENBIS, 'externalSampleName')
config_dict['laneCount'] = configParameters.get(OPENBIS, 'laneCount')
config_dict['kit'] = configParameters.get(OPENBIS, 'kit')
+ config_dict['10XSampleType'] = configParameters.get(OPENBIS, '10XSampleType')
+ config_dict['10XIndexSet'] = configParameters.get(OPENBIS, '10XIndexSet')
config_dict['headerSection'] = configParameters.get(ILLUMINA, 'headerSection')
config_dict['readsSection'] = configParameters.get(ILLUMINA, 'readsSection')
@@ -249,7 +251,7 @@ def get_vocabulary(vocabulary_code, service):
vocabulary_dict[term.getCode()] = term.getLabel()
else:
print ('No vocabulary found for ' + vocabulary_code)
- print(vocabulary_dict)
+# print(vocabulary_dict)
return vocabulary_dict
@@ -427,15 +429,25 @@ def get_contained_sample_properties(contained_samples, service, config_dict):
propertyDict[property] = parentProperties.get(property)
propertyDict['LANE'] = lane.getCode()
+ plain_lane = lane.getCode().split(':')[-1]
try:
- plain_lane = lane.getCode().split(':')[-1]
if barcodesPerLaneDict.has_key(plain_lane):
barcodesPerLaneDict[plain_lane].append(propertyDict[config_dict['index1Name']])
else:
barcodesPerLaneDict[plain_lane] = [propertyDict[config_dict['index1Name']]]
except:
- pass
+ pass
+
+ try:
+ if barcodesPerLaneDict.has_key(plain_lane):
+ barcodesPerLaneDict[plain_lane].append(propertyDict[config_dict['10XIndexSet']])
+ else:
+ barcodesPerLaneDict[plain_lane] = [propertyDict[config_dict['10XIndexSet']]]
+ except:
+ pass
+
+
myKey = sanitize_string(parentCode + '_' + lane.getCode())
parentDict[myKey] = propertyDict
@@ -449,6 +461,7 @@ def transform_sample_to_dict(foundFlowCell):
"""
flowCellDict = {}
fcProperties = foundFlowCell.getProperties()
+
for property in fcProperties:
flowCellDict[property] = fcProperties.get(property)
flowCellDict['Project'] = foundFlowCell.getExperimentIdentifierOrNull().split('/')[-1]
@@ -627,7 +640,7 @@ def verify_index_length (parentDict, flowCellDict, config_dict, logger):
return index_length_dict
-
+
def create_sample_sheet_dict(service, barcodesPerLaneDict, containedSamples, samplesPerLaneDict, model, parentDict, index_length_dict, flowCellDict,
config_dict, index1Vocabulary, index2Vocabulary, flowCellName, logger):
@@ -653,16 +666,25 @@ def create_sample_sheet_dict(service, barcodesPerLaneDict, containedSamples, sam
line = separator.join([lane_string + key, key + '_' + sanitize_string(lane_sample_properties[key][config_dict['externalSampleName']]), "", "", "", "", key, ""])
sampleSheetDict[lane_int + '_' + key] = [line]
single_index_set = True
-
+
for key in lane_sample_properties.keys():
# If no index or 'NOINDEX' assigned then just skip this sample
- if ((config_dict['index1Name'] not in lane_sample_properties[key] or lane_sample_properties[key][config_dict['index1Name']] == 'NOINDEX')):
+ if ((config_dict['index1Name'] not in lane_sample_properties[key] or lane_sample_properties[key][config_dict['index1Name']] == 'NOINDEX') and
+ config_dict['10XIndexSet'] not in lane_sample_properties[key]):
continue
- index1 = index1Vocabulary[lane_sample_properties[key][config_dict['index1Name']]]
+ index1 = ""
index2 = ""
+
+ if config_dict['index1Name'] in lane_sample_properties[key]:
+ index1 = lane_sample_properties[key][config_dict['index1Name']]
+
+ if config_dict['10XIndexSet'] in lane_sample_properties[key]:
+ index1 = lane_sample_properties[key][config_dict['10XIndexSet']]
+
+
if config_dict['index2Name'] in lane_sample_properties[key]:
index2 = lane_sample_properties[key][config_dict['index2Name']]
# Not needed, won't use it any more
--
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