diff --git a/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py b/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py
index 44ee4d3c7a9433733bf8f9895f1297579d04c750..bb9c2eb3d63f2799f4924bd76388f9821d5a93e0 100644
--- a/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py
+++ b/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq.py
@@ -1,6 +1,6 @@
'''
@copyright:
-Copyright 2015 ETH Zuerich, SIS
+Copyright 2016 ETH Zuerich, SIS
@license:
Licensed under the Apache License, Version 2.0 (the 'License');
@@ -664,13 +664,14 @@ def create_sample_sheet_dict(service, barcodesPerLaneDict, containedSamples, sam
index2=""
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
indexNumber = index2Vocabulary[lane_sample_properties[key][config_dict['index2Name']]].split()[2]
- try:
- kit = lane_sample_properties[key][config_dict['kit']]
- prefix = kitsDict[kit][0]
- except:
- prefix = ""
+ #try:
+ # kit = lane_sample_properties[key][config_dict['kit']]
+ # prefix = kitsDict[kit][0]
+ #except:
+ # prefix = ""
len_index1 = index_length_dict[int(lane_int)][0]
len_index2 = index_length_dict[int(lane_int)][1]
@@ -687,12 +688,12 @@ 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']]) + '_' + index1[0:len_index1] + '_' + index2[0:len_index2],
- "", "", index1Vocabulary[index1].split()[1], index1[0:len_index1], prefix + indexNumber, index2_processed, key, ""])
+ "", "","", index1[0:len_index1], indexNumber, index2_processed, key, ""])
sampleSheetDict[lane_int + '_' + key] = [line]
else:
line = separator.join([lane_string + key, key + '_' + sanitize_string(lane_sample_properties[key][config_dict['externalSampleName']]) + '_' + index1[0:len_index1],
- "", "", index1Vocabulary[index1].split()[1], index1[0:len_index1], key, ""])
+ "", "","", index1[0:len_index1], key, ""])
sampleSheetDict[lane_int + '_' + key] = [line]
csv_file_name = config_dict['SampleSheetFileName'] + '_' + flowCellName
diff --git a/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq_Test.py b/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq_Test.py
index d372a9465d7c2ea3ea8c66855539b21a6dc710f6..1b9336d5a8da3dce5b4c9c4826221d2c7f361d77 100644
--- a/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq_Test.py
+++ b/deep_sequencing_unit/source/Jython/createSampleSheet_bcl2fastq_Test.py
@@ -229,10 +229,10 @@ class create_sample_sheet_C7P5KANXX(unittest.TestCase):
self.index2Vocabulary, self.flowCellName, self.logger)
self.assertDictEqual(self.ordered_sample_sheet_dict,
- {u'8_BSSE_QGF_36781_C7P5KANXX_8': [u'8,BSSE_QGF_36781_C7P5KANXX_8,BSSE_QGF_36781_C7P5KANXX_8_Ribomethseq_mousecerebellum_comparison_CTTGTAA_NOINDEX,,,A012,CTTGTAA,(NoIndex),NOINDEX,BSSE_QGF_36781_C7P5KANXX_8,'],
- u'8_BSSE_QGF_36780_C7P5KANXX_8': [u'8,BSSE_QGF_36780_C7P5KANXX_8,BSSE_QGF_36780_C7P5KANXX_8_Ribomethseq_HEK_comparison_GCCAATA_NOINDEX,,,A006,GCCAATA,(NoIndex),NOINDEX,BSSE_QGF_36780_C7P5KANXX_8,'],
- u'8_BSSE_QGF_36552_C7P5KANXX_8': [u'8,BSSE_QGF_36552_C7P5KANXX_8,BSSE_QGF_36552_C7P5KANXX_8_CLIP_444_1_TGACCAA_NOINDEX,,,A004,TGACCAA,(NoIndex),NOINDEX,BSSE_QGF_36552_C7P5KANXX_8,'],
- u'8_BSSE_QGF_36779_C7P5KANXX_8': [u'8,BSSE_QGF_36779_C7P5KANXX_8,BSSE_QGF_36779_C7P5KANXX_8_HITS_CLIP_Fibrillarin_mouseNeurons_2_CAGATCA_NOINDEX,,,A007,CAGATCA,(NoIndex),NOINDEX,BSSE_QGF_36779_C7P5KANXX_8,']})
+ {u'8_BSSE_QGF_36781_C7P5KANXX_8': [u'8,BSSE_QGF_36781_C7P5KANXX_8,BSSE_QGF_36781_C7P5KANXX_8_Ribomethseq_mousecerebellum_comparison_CTTGTAA_NOINDEX,,,,CTTGTAA,(NoIndex),NOINDEX,BSSE_QGF_36781_C7P5KANXX_8,'],
+ u'8_BSSE_QGF_36780_C7P5KANXX_8': [u'8,BSSE_QGF_36780_C7P5KANXX_8,BSSE_QGF_36780_C7P5KANXX_8_Ribomethseq_HEK_comparison_GCCAATA_NOINDEX,,,,GCCAATA,(NoIndex),NOINDEX,BSSE_QGF_36780_C7P5KANXX_8,'],
+ u'8_BSSE_QGF_36552_C7P5KANXX_8': [u'8,BSSE_QGF_36552_C7P5KANXX_8,BSSE_QGF_36552_C7P5KANXX_8_CLIP_444_1_TGACCAA_NOINDEX,,,,TGACCAA,(NoIndex),NOINDEX,BSSE_QGF_36552_C7P5KANXX_8,'],
+ u'8_BSSE_QGF_36779_C7P5KANXX_8': [u'8,BSSE_QGF_36779_C7P5KANXX_8,BSSE_QGF_36779_C7P5KANXX_8_HITS_CLIP_Fibrillarin_mouseNeurons_2_CAGATCA_NOINDEX,,,,CAGATCA,(NoIndex),NOINDEX,BSSE_QGF_36779_C7P5KANXX_8,']})
def test_create_header_section(self):
@@ -328,22 +328,22 @@ class create_sample_sheet_HJWC3BGXX(unittest.TestCase):
self.index2Vocabulary, self.flowCellName, self.logger)
self.assertDictEqual(self.ordered_sample_sheet_dict,
- {u'1_BSSE_QGF_37098_HJWC3BGXX_1': [u'BSSE_QGF_37098_HJWC3BGXX_1,BSSE_QGF_37098_HJWC3BGXX_1_TB_358_PQR_2_0_GTTTCG,,,A021,GTTTCG,BSSE_QGF_37098_HJWC3BGXX_1,'],
- u'1_BSSE_QGF_37093_HJWC3BGXX_1': [u'BSSE_QGF_37093_HJWC3BGXX_1,BSSE_QGF_37093_HJWC3BGXX_1_TB_356_PQR_1_0_ATGTCA,,,A015,ATGTCA,BSSE_QGF_37093_HJWC3BGXX_1,'],
- u'1_BSSE_QGF_37094_HJWC3BGXX_1': [u'BSSE_QGF_37094_HJWC3BGXX_1,BSSE_QGF_37094_HJWC3BGXX_1_TB_357_BKM_1_0_CCGTCC,,,A016,CCGTCC,BSSE_QGF_37094_HJWC3BGXX_1,'],
- u'1_BSSE_QGF_37095_HJWC3BGXX_1': [u'BSSE_QGF_37095_HJWC3BGXX_1,BSSE_QGF_37095_HJWC3BGXX_1_TB_356_MTD_1_0_GTCCGC,,,A018,GTCCGC,BSSE_QGF_37095_HJWC3BGXX_1,'],
- u'1_BSSE_QGF_37087_HJWC3BGXX_1': [u'BSSE_QGF_37087_HJWC3BGXX_1,BSSE_QGF_37087_HJWC3BGXX_1_TB_355_DMSO1_GATCAG,,,A009,GATCAG,BSSE_QGF_37087_HJWC3BGXX_1,'],
- u'1_BSSE_QGF_37096_HJWC3BGXX_1': [u'BSSE_QGF_37096_HJWC3BGXX_1,BSSE_QGF_37096_HJWC3BGXX_1_TB_358_GDC_1_0_GTGAAA,,,A019,GTGAAA,BSSE_QGF_37096_HJWC3BGXX_1,'],
- u'1_BSSE_QGF_37092_HJWC3BGXX_1': [u'BSSE_QGF_37092_HJWC3BGXX_1,BSSE_QGF_37092_HJWC3BGXX_1_TB_357_COL_0_05_AGTTCC,,,A014,AGTTCC,BSSE_QGF_37092_HJWC3BGXX_1,'],
- u'1_BSSE_QGF_37088_HJWC3BGXX_1': [u'BSSE_QGF_37088_HJWC3BGXX_1,BSSE_QGF_37088_HJWC3BGXX_1_TB_355_PQR_0_5_TAGCTT,,,A010,TAGCTT,BSSE_QGF_37088_HJWC3BGXX_1,'],
- u'1_BSSE_QGF_37089_HJWC3BGXX_1': [u'BSSE_QGF_37089_HJWC3BGXX_1,BSSE_QGF_37089_HJWC3BGXX_1_TB_359_BKM_0_5_1_GGCTAC,,,A011,GGCTAC,BSSE_QGF_37089_HJWC3BGXX_1,'],
- u'1_BSSE_QGF_37101_HJWC3BGXX_1': [u'BSSE_QGF_37101_HJWC3BGXX_1,BSSE_QGF_37101_HJWC3BGXX_1_TB_357_GDC_2_0_ACTGAT,,,A025,ACTGAT,BSSE_QGF_37101_HJWC3BGXX_1,'],
- u'1_BSSE_QGF_37090_HJWC3BGXX_1': [u'BSSE_QGF_37090_HJWC3BGXX_1,BSSE_QGF_37090_HJWC3BGXX_1_TB_358_MTD_0_5_CTTGTA,,,A012,CTTGTA,BSSE_QGF_37090_HJWC3BGXX_1,'],
- u'1_BSSE_QGF_37099_HJWC3BGXX_1': [u'BSSE_QGF_37099_HJWC3BGXX_1,BSSE_QGF_37099_HJWC3BGXX_1_TB_360_BKM_2_0_1_CGTACG,,,A022,CGTACG,BSSE_QGF_37099_HJWC3BGXX_1,'],
- u'1_BSSE_QGF_37091_HJWC3BGXX_1': [u'BSSE_QGF_37091_HJWC3BGXX_1,BSSE_QGF_37091_HJWC3BGXX_1_TB_358_GDC_0_5_AGTCAA,,,A013,AGTCAA,BSSE_QGF_37091_HJWC3BGXX_1,'],
- u'1_BSSE_QGF_37102_HJWC3BGXX_1': [u'BSSE_QGF_37102_HJWC3BGXX_1,BSSE_QGF_37102_HJWC3BGXX_1_TB_361_COL_0_2_1_ATTCCT,,,A027,ATTCCT,BSSE_QGF_37102_HJWC3BGXX_1,'],
- u'1_BSSE_QGF_37100_HJWC3BGXX_1': [u'BSSE_QGF_37100_HJWC3BGXX_1,BSSE_QGF_37100_HJWC3BGXX_1_TB_357_MTD_2_0_GAGTGG,,,A023,GAGTGG,BSSE_QGF_37100_HJWC3BGXX_1,'],
- u'1_BSSE_QGF_37097_HJWC3BGXX_1': [u'BSSE_QGF_37097_HJWC3BGXX_1,BSSE_QGF_37097_HJWC3BGXX_1_TB_358_COL_0_1_GTGGCC,,,A020,GTGGCC,BSSE_QGF_37097_HJWC3BGXX_1,']})
+ {u'1_BSSE_QGF_37098_HJWC3BGXX_1': [u'BSSE_QGF_37098_HJWC3BGXX_1,BSSE_QGF_37098_HJWC3BGXX_1_TB_358_PQR_2_0_GTTTCG,,,,GTTTCG,BSSE_QGF_37098_HJWC3BGXX_1,'],
+ u'1_BSSE_QGF_37093_HJWC3BGXX_1': [u'BSSE_QGF_37093_HJWC3BGXX_1,BSSE_QGF_37093_HJWC3BGXX_1_TB_356_PQR_1_0_ATGTCA,,,,ATGTCA,BSSE_QGF_37093_HJWC3BGXX_1,'],
+ u'1_BSSE_QGF_37094_HJWC3BGXX_1': [u'BSSE_QGF_37094_HJWC3BGXX_1,BSSE_QGF_37094_HJWC3BGXX_1_TB_357_BKM_1_0_CCGTCC,,,,CCGTCC,BSSE_QGF_37094_HJWC3BGXX_1,'],
+ u'1_BSSE_QGF_37095_HJWC3BGXX_1': [u'BSSE_QGF_37095_HJWC3BGXX_1,BSSE_QGF_37095_HJWC3BGXX_1_TB_356_MTD_1_0_GTCCGC,,,,GTCCGC,BSSE_QGF_37095_HJWC3BGXX_1,'],
+ u'1_BSSE_QGF_37087_HJWC3BGXX_1': [u'BSSE_QGF_37087_HJWC3BGXX_1,BSSE_QGF_37087_HJWC3BGXX_1_TB_355_DMSO1_GATCAG,,,,GATCAG,BSSE_QGF_37087_HJWC3BGXX_1,'],
+ u'1_BSSE_QGF_37096_HJWC3BGXX_1': [u'BSSE_QGF_37096_HJWC3BGXX_1,BSSE_QGF_37096_HJWC3BGXX_1_TB_358_GDC_1_0_GTGAAA,,,,GTGAAA,BSSE_QGF_37096_HJWC3BGXX_1,'],
+ u'1_BSSE_QGF_37092_HJWC3BGXX_1': [u'BSSE_QGF_37092_HJWC3BGXX_1,BSSE_QGF_37092_HJWC3BGXX_1_TB_357_COL_0_05_AGTTCC,,,,AGTTCC,BSSE_QGF_37092_HJWC3BGXX_1,'],
+ u'1_BSSE_QGF_37088_HJWC3BGXX_1': [u'BSSE_QGF_37088_HJWC3BGXX_1,BSSE_QGF_37088_HJWC3BGXX_1_TB_355_PQR_0_5_TAGCTT,,,,TAGCTT,BSSE_QGF_37088_HJWC3BGXX_1,'],
+ u'1_BSSE_QGF_37089_HJWC3BGXX_1': [u'BSSE_QGF_37089_HJWC3BGXX_1,BSSE_QGF_37089_HJWC3BGXX_1_TB_359_BKM_0_5_1_GGCTAC,,,,GGCTAC,BSSE_QGF_37089_HJWC3BGXX_1,'],
+ u'1_BSSE_QGF_37101_HJWC3BGXX_1': [u'BSSE_QGF_37101_HJWC3BGXX_1,BSSE_QGF_37101_HJWC3BGXX_1_TB_357_GDC_2_0_ACTGAT,,,,ACTGAT,BSSE_QGF_37101_HJWC3BGXX_1,'],
+ u'1_BSSE_QGF_37090_HJWC3BGXX_1': [u'BSSE_QGF_37090_HJWC3BGXX_1,BSSE_QGF_37090_HJWC3BGXX_1_TB_358_MTD_0_5_CTTGTA,,,,CTTGTA,BSSE_QGF_37090_HJWC3BGXX_1,'],
+ u'1_BSSE_QGF_37099_HJWC3BGXX_1': [u'BSSE_QGF_37099_HJWC3BGXX_1,BSSE_QGF_37099_HJWC3BGXX_1_TB_360_BKM_2_0_1_CGTACG,,,,CGTACG,BSSE_QGF_37099_HJWC3BGXX_1,'],
+ u'1_BSSE_QGF_37091_HJWC3BGXX_1': [u'BSSE_QGF_37091_HJWC3BGXX_1,BSSE_QGF_37091_HJWC3BGXX_1_TB_358_GDC_0_5_AGTCAA,,,,AGTCAA,BSSE_QGF_37091_HJWC3BGXX_1,'],
+ u'1_BSSE_QGF_37102_HJWC3BGXX_1': [u'BSSE_QGF_37102_HJWC3BGXX_1,BSSE_QGF_37102_HJWC3BGXX_1_TB_361_COL_0_2_1_ATTCCT,,,,ATTCCT,BSSE_QGF_37102_HJWC3BGXX_1,'],
+ u'1_BSSE_QGF_37100_HJWC3BGXX_1': [u'BSSE_QGF_37100_HJWC3BGXX_1,BSSE_QGF_37100_HJWC3BGXX_1_TB_357_MTD_2_0_GAGTGG,,,,GAGTGG,BSSE_QGF_37100_HJWC3BGXX_1,'],
+ u'1_BSSE_QGF_37097_HJWC3BGXX_1': [u'BSSE_QGF_37097_HJWC3BGXX_1,BSSE_QGF_37097_HJWC3BGXX_1_TB_358_COL_0_1_GTGGCC,,,,GTGGCC,BSSE_QGF_37097_HJWC3BGXX_1,']})
def test_create_header_section(self):
self.model = get_model(self.flowCellDict['RUN_NAME_FOLDER'])
@@ -438,14 +438,14 @@ class create_sample_sheet_000000000_AH5W3(unittest.TestCase):
self.assertDictEqual(self.ordered_sample_sheet_dict,
- {u'1_BSSE_QGF_36763_000000000_AH5W3_1': [u'1,BSSE_QGF_36763_000000000_AH5W3_1,BSSE_QGF_36763_000000000_AH5W3_1_H7_PRE_Idx_15_ATGTCA,,,A015,ATGTCA,BSSE_QGF_36763_000000000_AH5W3_1,'],
- u'1_BSSE_QGF_36765_000000000_AH5W3_1': [u'1,BSSE_QGF_36765_000000000_AH5W3_1,BSSE_QGF_36765_000000000_AH5W3_1_H8_NBC_Idx_16_CCGTCC,,,A016,CCGTCC,BSSE_QGF_36765_000000000_AH5W3_1,'],
- u'1_BSSE_QGF_36768_000000000_AH5W3_1': [u'1,BSSE_QGF_36768_000000000_AH5W3_1,BSSE_QGF_36768_000000000_AH5W3_1_H8_BMPC_Idx_19_GTGAAA,,,A019,GTGAAA,BSSE_QGF_36768_000000000_AH5W3_1,'],
- u'1_BSSE_QGF_36767_000000000_AH5W3_1': [u'1,BSSE_QGF_36767_000000000_AH5W3_1,BSSE_QGF_36767_000000000_AH5W3_1_H8_PRE_Idx_20_GTGGCC,,,A020,GTGGCC,BSSE_QGF_36767_000000000_AH5W3_1,'],
- u'1_BSSE_QGF_36766_000000000_AH5W3_1': [u'1,BSSE_QGF_36766_000000000_AH5W3_1,BSSE_QGF_36766_000000000_AH5W3_1_H8_SPC_Idx_18_GTCCGC,,,A018,GTCCGC,BSSE_QGF_36766_000000000_AH5W3_1,'],
- u'1_BSSE_QGF_36761_000000000_AH5W3_1': [u'1,BSSE_QGF_36761_000000000_AH5W3_1,BSSE_QGF_36761_000000000_AH5W3_1_H7_NBC_Idx_12_CTTGTA,,,A012,CTTGTA,BSSE_QGF_36761_000000000_AH5W3_1,'],
- u'1_BSSE_QGF_36762_000000000_AH5W3_1': [u'1,BSSE_QGF_36762_000000000_AH5W3_1,BSSE_QGF_36762_000000000_AH5W3_1_H7_SPC_Idx_13_AGTCAA,,,A013,AGTCAA,BSSE_QGF_36762_000000000_AH5W3_1,'],
- u'1_BSSE_QGF_36764_000000000_AH5W3_1': [u'1,BSSE_QGF_36764_000000000_AH5W3_1,BSSE_QGF_36764_000000000_AH5W3_1_H7_BMPC_Idx_14_AGTTCC,,,A014,AGTTCC,BSSE_QGF_36764_000000000_AH5W3_1,']})
+ {u'1_BSSE_QGF_36763_000000000_AH5W3_1': [u'1,BSSE_QGF_36763_000000000_AH5W3_1,BSSE_QGF_36763_000000000_AH5W3_1_H7_PRE_Idx_15_ATGTCA,,,,ATGTCA,BSSE_QGF_36763_000000000_AH5W3_1,'],
+ u'1_BSSE_QGF_36765_000000000_AH5W3_1': [u'1,BSSE_QGF_36765_000000000_AH5W3_1,BSSE_QGF_36765_000000000_AH5W3_1_H8_NBC_Idx_16_CCGTCC,,,,CCGTCC,BSSE_QGF_36765_000000000_AH5W3_1,'],
+ u'1_BSSE_QGF_36768_000000000_AH5W3_1': [u'1,BSSE_QGF_36768_000000000_AH5W3_1,BSSE_QGF_36768_000000000_AH5W3_1_H8_BMPC_Idx_19_GTGAAA,,,,GTGAAA,BSSE_QGF_36768_000000000_AH5W3_1,'],
+ u'1_BSSE_QGF_36767_000000000_AH5W3_1': [u'1,BSSE_QGF_36767_000000000_AH5W3_1,BSSE_QGF_36767_000000000_AH5W3_1_H8_PRE_Idx_20_GTGGCC,,,,GTGGCC,BSSE_QGF_36767_000000000_AH5W3_1,'],
+ u'1_BSSE_QGF_36766_000000000_AH5W3_1': [u'1,BSSE_QGF_36766_000000000_AH5W3_1,BSSE_QGF_36766_000000000_AH5W3_1_H8_SPC_Idx_18_GTCCGC,,,,GTCCGC,BSSE_QGF_36766_000000000_AH5W3_1,'],
+ u'1_BSSE_QGF_36761_000000000_AH5W3_1': [u'1,BSSE_QGF_36761_000000000_AH5W3_1,BSSE_QGF_36761_000000000_AH5W3_1_H7_NBC_Idx_12_CTTGTA,,,,CTTGTA,BSSE_QGF_36761_000000000_AH5W3_1,'],
+ u'1_BSSE_QGF_36762_000000000_AH5W3_1': [u'1,BSSE_QGF_36762_000000000_AH5W3_1,BSSE_QGF_36762_000000000_AH5W3_1_H7_SPC_Idx_13_AGTCAA,,,,AGTCAA,BSSE_QGF_36762_000000000_AH5W3_1,'],
+ u'1_BSSE_QGF_36764_000000000_AH5W3_1': [u'1,BSSE_QGF_36764_000000000_AH5W3_1,BSSE_QGF_36764_000000000_AH5W3_1_H7_BMPC_Idx_14_AGTTCC,,,,AGTTCC,BSSE_QGF_36764_000000000_AH5W3_1,']})
def test_create_header_section(self):