From 145d81b9ead0296150e0066f2252e534327f8ef3 Mon Sep 17 00:00:00 2001 From: chuan-wang Date: Tue, 27 Oct 2020 13:25:56 +0100 Subject: [PATCH 1/2] Change the way how samples are sorted --- taca/illumina/HiSeqX_Runs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/taca/illumina/HiSeqX_Runs.py b/taca/illumina/HiSeqX_Runs.py index fc76dbb7..eb312088 100755 --- a/taca/illumina/HiSeqX_Runs.py +++ b/taca/illumina/HiSeqX_Runs.py @@ -374,8 +374,8 @@ def _generate_clean_samplesheet(ssparser, indexfile, fields_to_remove=None, rena sample['index2'] = index_dict_smartseq[smartseq_index][x][1] # Sort to get the added indicies from 10x in the right place - # Python 3 doesn't support sorting a list of dicts implicitly. Sort by lane and then index - ssparser.data.sort(key=lambda item: (item.get('Lane'), item.get('index'))) + # Python 3 doesn't support sorting a list of dicts implicitly. Sort by lane and then Sample_ID + ssparser.data.sort(key=lambda item: (item.get('Lane'), item.get('Sample_ID'))) if not fields_to_remove: fields_to_remove = [] From cdb0aeee521cd954d34c16f46321d3b168bbf603 Mon Sep 17 00:00:00 2001 From: chuan-wang Date: Tue, 27 Oct 2020 16:10:36 +0100 Subject: [PATCH 2/2] Fix tests --- tests/data/2014/FCIDXX.csv | 2 +- tests/test_illumina.py | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/data/2014/FCIDXX.csv b/tests/data/2014/FCIDXX.csv index 62a0ac2c..f807e47e 100644 --- a/tests/data/2014/FCIDXX.csv +++ b/tests/data/2014/FCIDXX.csv @@ -6,7 +6,7 @@ Experiment Name,CIDXX 151 151 [Data] -Lane,SampleID,SampleName,SamplePlate,SampleWell,index,index2,Project,Description +Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,index,index2,Project,Description 1,Sample_P10000_1001,P10000_1001,CIDXX,1:1,SI-GA-A1,,A_Test_18_01, 2,Sample_P10000_1005,P10000_1005,CIDXX,2:1,AGGTACC,,A_Test_18_01, 3,Sample_P10000_1006,P10000_1006,CIDXX,3:1,SMARTSEQ-1A,,A_Test_18_01, diff --git a/tests/test_illumina.py b/tests/test_illumina.py index cfb4d06b..30e5ebee 100644 --- a/tests/test_illumina.py +++ b/tests/test_illumina.py @@ -731,16 +731,16 @@ def test_generate_clean_samplesheet(self): Experiment Name,CIDXX Investigator Name,Test [Data] -Lane,SampleID,SampleName,SamplePlate,SampleWell,index,index2,Project,Description +Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,index,index2,Project,Description 1,Sample_P10000_1001,P10000_1001,CIDXX,1:1,AACCGTAA,,A_Test_18_01, -1,Sample_P10000_1001,P10000_1001,CIDXX,1:1,CTAAACGG,,A_Test_18_01, 1,Sample_P10000_1001,P10000_1001,CIDXX,1:1,GGTTTACT,,A_Test_18_01, +1,Sample_P10000_1001,P10000_1001,CIDXX,1:1,CTAAACGG,,A_Test_18_01, 1,Sample_P10000_1001,P10000_1001,CIDXX,1:1,TCGGCGTC,,A_Test_18_01, 2,Sample_P10000_1005,P10000_1005,CIDXX,2:1,AGGTACC,,A_Test_18_01, +3,Sample_P10000_1006,P10000_1006,CIDXX,3:1,TGTATCCGAA,CACAGGTGAA,A_Test_18_01, 3,Sample_P10000_1006,P10000_1006,CIDXX,3:1,GAGCGCCTAT,TTGGTACGCG,A_Test_18_01, -3,Sample_P10000_1006,P10000_1006,CIDXX,3:1,GCTAGGTCAA,CACAGGTGAA,A_Test_18_01, 3,Sample_P10000_1006,P10000_1006,CIDXX,3:1,TAAGACGGTG,TTGGTACGCG,A_Test_18_01, -3,Sample_P10000_1006,P10000_1006,CIDXX,3:1,TGTATCCGAA,CACAGGTGAA,A_Test_18_01, +3,Sample_P10000_1006,P10000_1006,CIDXX,3:1,GCTAGGTCAA,CACAGGTGAA,A_Test_18_01, 4,Sample_P10000_1007,P10000_1007,CIDXX,4:1,GTAACATGCG,AGTGTTACCT,A_Test_18_01, ''' got_samplesheet = _generate_clean_samplesheet(ssparser, indexfile, rename_samples=True, rename_qPCR_suffix = True, fields_qPCR=[ssparser.dfield_snm]) @@ -893,7 +893,7 @@ def test_generate_samplesheet_subset(self): Experiment Name,CIDXX Investigator Name,Test [Data] -Lane,SampleID,SampleName,SamplePlate,SampleWell,index,index2,Project,Description +Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,index,index2,Project,Description 1,Sample_P10000_1001,P10000_1001,CIDXX,1:1,SI-GA-A1,,A_Test_18_01, ''' self.assertEqual(got_data, expected_data)