From f22ce1b4f563ad60974b47145d1848e3aa2f603b Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Mon, 4 Dec 2017 16:16:03 +0000
Subject: [PATCH] write a marker file when it is a 10x run
SVN: 39004
---
.../Jython/createSampleSheet_bcl2fastq.py | 20 ++++++++++++++-----
1 file changed, 15 insertions(+), 5 deletions(-)
diff --git a/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py b/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py
index 5de03e3342b..a3b321c76f3 100644
--- a/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py
+++ b/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py
@@ -199,6 +199,7 @@ def readConfig(logger):
config_dict['kit'] = configParameters.get(OPENBIS, 'kit')
config_dict['10XSampleType'] = configParameters.get(OPENBIS, '10XSampleType')
config_dict['10XIndexSet'] = configParameters.get(OPENBIS, '10XIndexSet')
+ config_dict['recovered_cells'] = configParameters.get(OPENBIS, 'recovered_cells')
config_dict['headerSection'] = configParameters.get(ILLUMINA, 'headerSection')
config_dict['readsSection'] = configParameters.get(ILLUMINA, 'readsSection')
@@ -446,8 +447,6 @@ def get_contained_sample_properties(contained_samples, service, config_dict):
barcodesPerLaneDict[plain_lane] = [propertyDict[config_dict['10XIndexSet']]]
except:
pass
-
-
myKey = sanitize_string(parentCode + '_' + lane.getCode())
parentDict[myKey] = propertyDict
@@ -497,6 +496,12 @@ def write_sample_sheet_single_lane(model, ordered_sample_sheet_dict, flowCellDic
logger.error('File error: ' + str(err))
print ('File error: ' + str(err))
+def write_marker_file(flowCellDict, myoptions):
+ marker_file_path = myoptions.outdir + ".10x_run_" + flowCellDict['Name']
+ with open(marker_file_path, 'wb') as marker_file:
+ for flowcell_prop in flowCellDict:
+ marker_file.write(flowcell_prop)
+
def create_header_section (model, config_dict, parentDict, flowCellDict, index_length_dict, lane):
@@ -528,7 +533,6 @@ def create_header_section (model, config_dict, parentDict, flowCellDict, index_l
len_index1 = index_length_dict[int(lane)][0]
len_index2 = index_length_dict[int(lane)][1]
-
# here we take the first sample to determine the Sample Prep Kit
try:
@@ -550,6 +554,8 @@ def create_header_section (model, config_dict, parentDict, flowCellDict, index_l
header_list.append(header_section.pop().strip() + separator + assay)
header_list.append(header_section.pop().strip() + separator + flowCellDict[config_dict['endType']] + '_' + flowCellDict[config_dict['cycles']])
header_list.append(header_section.pop().strip() + separator + config_dict['chemistry'])
+# if config_dict['10XIndexSet']:
+# header_list.append(config_dict['recovered_cells'])
header_list.append('')
reads_section = config_dict['readsSection'].split(separator)
@@ -645,6 +651,7 @@ def create_sample_sheet_dict(service, barcodesPerLaneDict, containedSamples, sam
config_dict, index1Vocabulary, index2Vocabulary, flowCellName, logger):
sampleSheetDict = {}
+ _10_run = False
separator = config_dict['separator']
for lane in containedSamples:
@@ -686,6 +693,7 @@ def create_sample_sheet_dict(service, barcodesPerLaneDict, containedSamples, sam
index1 = lane_sample_properties[key][config_dict['10XIndexSet']]
# Do not modify the index length, as these are index sets provided by 10x
len_index1 = len(index1)
+ _10_run = True
if config_dict['index2Name'] in lane_sample_properties[key]:
index2 = lane_sample_properties[key][config_dict['index2Name']]
@@ -723,7 +731,7 @@ def create_sample_sheet_dict(service, barcodesPerLaneDict, containedSamples, sam
csv_file_name = config_dict['SampleSheetFileName'] + '_' + flowCellName
ordered_sample_sheet_dict = OrderedDict(sorted(sampleSheetDict.items(), key=lambda t: t[0]))
- return ordered_sample_sheet_dict, csv_file_name
+ return _10_run, ordered_sample_sheet_dict, csv_file_name
'''
Main script
@@ -756,7 +764,7 @@ def main ():
index1Vocabulary = get_vocabulary(config_dict['index1Name'], service)
index2Vocabulary = get_vocabulary(config_dict['index2Name'], service)
index_length_dict = verify_index_length(parentDict, flowCellDict, config_dict, logger)
- ordered_sample_sheet_dict, csv_file_name = create_sample_sheet_dict(service, barcodesPerLaneDict, containedSamples,
+ _10_run, ordered_sample_sheet_dict, csv_file_name = create_sample_sheet_dict(service, barcodesPerLaneDict, containedSamples,
samplesPerLaneDict, model, parentDict, index_length_dict,
flowCellDict, config_dict, index1Vocabulary, index2Vocabulary,
flowCellName, logger)
@@ -769,6 +777,8 @@ def main ():
else:
write_sample_sheet_single_lane(model, ordered_sample_sheet_dict, flowCellDict, index_length_dict,
parentDict, config_dict, myoptions, logger, csv_file_name)
+ if _10_run:
+ write_marker_file(flowCellDict, myoptions)
logout(service, logger)
--
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