From fc01f25642637d8d89eda93d2b1ffba5d2001188 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Mon, 7 Jan 2013 17:46:06 -0800 Subject: [PATCH] Add unaligned stats files to hiseq test case --- .../pipelines/test/simulate_runfolder.py | 11 + .../pipelines/test/test_runfolder_rta1_12.py | 1 + .../test/testdata/1_12/basecall_stats/All.htm | 496 +++++++++++++++++ .../1_12/basecall_stats/Demultiplex_Stats.htm | 517 ++++++++++++++++++ .../test/testdata/1_12/basecall_stats/IVC.htm | 9 + 5 files changed, 1034 insertions(+) create mode 100644 htsworkflow/pipelines/test/testdata/1_12/basecall_stats/All.htm create mode 100644 htsworkflow/pipelines/test/testdata/1_12/basecall_stats/Demultiplex_Stats.htm create mode 100644 htsworkflow/pipelines/test/testdata/1_12/basecall_stats/IVC.htm diff --git a/htsworkflow/pipelines/test/simulate_runfolder.py b/htsworkflow/pipelines/test/simulate_runfolder.py index afa2edf..759a13e 100644 --- a/htsworkflow/pipelines/test/simulate_runfolder.py +++ b/htsworkflow/pipelines/test/simulate_runfolder.py @@ -100,6 +100,17 @@ def make_unaligned_config_1_12(unaligned_dir): ] for src, dest in demultiplex_pairs: shutil.copy(src, dest) + +def make_unaligned_status_1_12(unaligned_dir, flowcell_id): + basecall_status = ['All.htm', 'Demultiplex_Stats.htm', 'IVC.htm'] + test_data_root = os.path.join(TESTDATA_DIR, '1_12', 'basecall_stats') + basecall_stats = os.path.join(unaligned_dir, + 'Basecall_Stats_{0}'.format(flowcell_id)) + os.mkdir(basecall_stats) + for filename in basecall_status: + source = os.path.join(test_data_root, filename) + destination = os.path.join(basecall_stats, filename) + shutil.copy(source, destination) def make_rta_intensities_1460(data_dir, version='1.4.6.0'): """ diff --git a/htsworkflow/pipelines/test/test_runfolder_rta1_12.py b/htsworkflow/pipelines/test/test_runfolder_rta1_12.py index 6933157..2a64b4f 100644 --- a/htsworkflow/pipelines/test/test_runfolder_rta1_12.py +++ b/htsworkflow/pipelines/test/test_runfolder_rta1_12.py @@ -46,6 +46,7 @@ def make_runfolder(obj=None): os.mkdir(unaligned_dir) make_unaligned_fastqs_1_12(unaligned_dir, flowcell_id) make_unaligned_config_1_12(unaligned_dir) + make_unaligned_status_1_12(unaligned_dir, flowcell_id) aligned_dir = os.path.join(runfolder_dir, "Aligned") os.mkdir(aligned_dir) diff --git a/htsworkflow/pipelines/test/testdata/1_12/basecall_stats/All.htm b/htsworkflow/pipelines/test/testdata/1_12/basecall_stats/All.htm new file mode 100644 index 0000000..3e3efa6 --- /dev/null +++ b/htsworkflow/pipelines/test/testdata/1_12/basecall_stats/All.htm @@ -0,0 +1,496 @@ + + + + + +120406_SN787_0114_AD0PMDACXX All

120406_SN787_0114_AD0PMDACXX All

+ +Full output (Warning: may overload your browser!)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TileLane 1Lane 2Lane 3
1101Plots/s_1_1101_all.pngPlots/s_2_1101_all.pngPlots/s_3_1101_all.png
1102Plots/s_1_1102_all.pngPlots/s_2_1102_all.pngPlots/s_3_1102_all.png
1103Plots/s_1_1103_all.pngPlots/s_2_1103_all.pngPlots/s_3_1103_all.png
1104Plots/s_1_1104_all.pngPlots/s_2_1104_all.pngPlots/s_3_1104_all.png
1105
1106Plots/s_1_1106_all.pngPlots/s_2_1106_all.pngPlots/s_3_1106_all.png
1107Plots/s_1_1107_all.pngPlots/s_2_1107_all.pngPlots/s_3_1107_all.png
1108Plots/s_1_1108_all.pngPlots/s_2_1108_all.pngPlots/s_3_1108_all.png
1109Plots/s_1_1109_all.pngPlots/s_2_1109_all.pngPlots/s_3_1109_all.png
1110
1111Plots/s_1_1111_all.pngPlots/s_2_1111_all.pngPlots/s_3_1111_all.png
1112Plots/s_1_1112_all.pngPlots/s_2_1112_all.pngPlots/s_3_1112_all.png
1113Plots/s_1_1113_all.pngPlots/s_2_1113_all.pngPlots/s_3_1113_all.png
1114Plots/s_1_1114_all.pngPlots/s_2_1114_all.pngPlots/s_3_1114_all.png
1115
1116Plots/s_1_1116_all.pngPlots/s_2_1116_all.pngPlots/s_3_1116_all.png
1201Plots/s_1_1201_all.pngPlots/s_2_1201_all.pngPlots/s_3_1201_all.png
1202Plots/s_1_1202_all.pngPlots/s_2_1202_all.pngPlots/s_3_1202_all.png
1203Plots/s_1_1203_all.pngPlots/s_2_1203_all.pngPlots/s_3_1203_all.png
1204
1205Plots/s_1_1205_all.pngPlots/s_2_1205_all.pngPlots/s_3_1205_all.png
1206Plots/s_1_1206_all.pngPlots/s_2_1206_all.pngPlots/s_3_1206_all.png
1207Plots/s_1_1207_all.pngPlots/s_2_1207_all.pngPlots/s_3_1207_all.png
1208Plots/s_1_1208_all.pngPlots/s_2_1208_all.pngPlots/s_3_1208_all.png
1209
1210Plots/s_1_1210_all.pngPlots/s_2_1210_all.pngPlots/s_3_1210_all.png
1211Plots/s_1_1211_all.pngPlots/s_2_1211_all.pngPlots/s_3_1211_all.png
1212Plots/s_1_1212_all.pngPlots/s_2_1212_all.pngPlots/s_3_1212_all.png
1213Plots/s_1_1213_all.pngPlots/s_2_1213_all.pngPlots/s_3_1213_all.png
1214
1215Plots/s_1_1215_all.pngPlots/s_2_1215_all.pngPlots/s_3_1215_all.png
1216Plots/s_1_1216_all.pngPlots/s_2_1216_all.pngPlots/s_3_1216_all.png
1301Plots/s_1_1301_all.pngPlots/s_2_1301_all.pngPlots/s_3_1301_all.png
1302Plots/s_1_1302_all.pngPlots/s_2_1302_all.pngPlots/s_3_1302_all.png
1303
1304Plots/s_1_1304_all.pngPlots/s_2_1304_all.pngPlots/s_3_1304_all.png
1305Plots/s_1_1305_all.pngPlots/s_2_1305_all.pngPlots/s_3_1305_all.png
1306Plots/s_1_1306_all.pngPlots/s_2_1306_all.pngPlots/s_3_1306_all.png
1307Plots/s_1_1307_all.pngPlots/s_2_1307_all.pngPlots/s_3_1307_all.png
1308
1309Plots/s_1_1309_all.pngPlots/s_2_1309_all.pngPlots/s_3_1309_all.png
1310Plots/s_1_1310_all.pngPlots/s_2_1310_all.pngPlots/s_3_1310_all.png
1311Plots/s_1_1311_all.pngPlots/s_2_1311_all.pngPlots/s_3_1311_all.png
1312Plots/s_1_1312_all.pngPlots/s_2_1312_all.pngPlots/s_3_1312_all.png
1313
1314Plots/s_1_1314_all.pngPlots/s_2_1314_all.pngPlots/s_3_1314_all.png
1315Plots/s_1_1315_all.pngPlots/s_2_1315_all.pngPlots/s_3_1315_all.png
1316Plots/s_1_1316_all.pngPlots/s_2_1316_all.pngPlots/s_3_1316_all.png
2101Plots/s_1_2101_all.pngPlots/s_2_2101_all.pngPlots/s_3_2101_all.png
2102
2103Plots/s_1_2103_all.pngPlots/s_2_2103_all.pngPlots/s_3_2103_all.png
2104Plots/s_1_2104_all.pngPlots/s_2_2104_all.pngPlots/s_3_2104_all.png
2105Plots/s_1_2105_all.pngPlots/s_2_2105_all.pngPlots/s_3_2105_all.png
2106Plots/s_1_2106_all.pngPlots/s_2_2106_all.pngPlots/s_3_2106_all.png
2107
2108Plots/s_1_2108_all.pngPlots/s_2_2108_all.pngPlots/s_3_2108_all.png
2109Plots/s_1_2109_all.pngPlots/s_2_2109_all.pngPlots/s_3_2109_all.png
2110Plots/s_1_2110_all.pngPlots/s_2_2110_all.pngPlots/s_3_2110_all.png
2111Plots/s_1_2111_all.pngPlots/s_2_2111_all.pngPlots/s_3_2111_all.png
2112
2113Plots/s_1_2113_all.pngPlots/s_2_2113_all.pngPlots/s_3_2113_all.png
2114Plots/s_1_2114_all.pngPlots/s_2_2114_all.pngPlots/s_3_2114_all.png
2115Plots/s_1_2115_all.pngPlots/s_2_2115_all.pngPlots/s_3_2115_all.png
2116Plots/s_1_2116_all.pngPlots/s_2_2116_all.pngPlots/s_3_2116_all.png
2201
2202Plots/s_1_2202_all.pngPlots/s_2_2202_all.pngPlots/s_3_2202_all.png
2203Plots/s_1_2203_all.pngPlots/s_2_2203_all.pngPlots/s_3_2203_all.png
2204Plots/s_1_2204_all.pngPlots/s_2_2204_all.pngPlots/s_3_2204_all.png
2205Plots/s_1_2205_all.pngPlots/s_2_2205_all.pngPlots/s_3_2205_all.png
2206
2207Plots/s_1_2207_all.pngPlots/s_2_2207_all.pngPlots/s_3_2207_all.png
2208Plots/s_1_2208_all.pngPlots/s_2_2208_all.pngPlots/s_3_2208_all.png
2209Plots/s_1_2209_all.pngPlots/s_2_2209_all.pngPlots/s_3_2209_all.png
2210Plots/s_1_2210_all.pngPlots/s_2_2210_all.pngPlots/s_3_2210_all.png
2211
2212Plots/s_1_2212_all.pngPlots/s_2_2212_all.pngPlots/s_3_2212_all.png
2213Plots/s_1_2213_all.pngPlots/s_2_2213_all.pngPlots/s_3_2213_all.png
2214Plots/s_1_2214_all.pngPlots/s_2_2214_all.pngPlots/s_3_2214_all.png
2215Plots/s_1_2215_all.pngPlots/s_2_2215_all.pngPlots/s_3_2215_all.png
2216
2301Plots/s_1_2301_all.pngPlots/s_2_2301_all.pngPlots/s_3_2301_all.png
2302Plots/s_1_2302_all.pngPlots/s_2_2302_all.pngPlots/s_3_2302_all.png
2303Plots/s_1_2303_all.pngPlots/s_2_2303_all.pngPlots/s_3_2303_all.png
2304Plots/s_1_2304_all.pngPlots/s_2_2304_all.pngPlots/s_3_2304_all.png
2305
2306Plots/s_1_2306_all.pngPlots/s_2_2306_all.pngPlots/s_3_2306_all.png
2307Plots/s_1_2307_all.pngPlots/s_2_2307_all.pngPlots/s_3_2307_all.png
2308Plots/s_1_2308_all.pngPlots/s_2_2308_all.pngPlots/s_3_2308_all.png
2309Plots/s_1_2309_all.pngPlots/s_2_2309_all.pngPlots/s_3_2309_all.png
2310
2311Plots/s_1_2311_all.pngPlots/s_2_2311_all.pngPlots/s_3_2311_all.png
2312Plots/s_1_2312_all.pngPlots/s_2_2312_all.pngPlots/s_3_2312_all.png
2313Plots/s_1_2313_all.pngPlots/s_2_2313_all.pngPlots/s_3_2313_all.png
2314Plots/s_1_2314_all.pngPlots/s_2_2314_all.pngPlots/s_3_2314_all.png
2315
2316Plots/s_1_2316_all.pngPlots/s_2_2316_all.pngPlots/s_3_2316_all.png
+ + diff --git a/htsworkflow/pipelines/test/testdata/1_12/basecall_stats/Demultiplex_Stats.htm b/htsworkflow/pipelines/test/testdata/1_12/basecall_stats/Demultiplex_Stats.htm new file mode 100644 index 0000000..fc98d6e --- /dev/null +++ b/htsworkflow/pipelines/test/testdata/1_12/basecall_stats/Demultiplex_Stats.htm @@ -0,0 +1,517 @@ + + + + +

Flowcell: D0PMDACXX

+

Barcode lane statistics

+
++++++++++++++++ + + + + + + + + + + + + + + + + +
LaneSample IDSample RefIndexDescriptionControlProjectYield (Mbases)% PF# Reads% of raw clusters per lane% Perfect Index Reads% One Mismatch Reads (Index)% of >= Q30 Bases (PF)Mean Quality Score (PF)
+
++++++++++++++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
112812Mus_musculusTAAGGCGAES 10pg Nxt 701 503N128121,68297.1317,320,10015.05100.000.0093.5936.23
112813Mus_musculusCGTACTAGES 10pg Nxt 702 504N128132,34097.6623,962,11920.82100.000.0093.5336.16
112814Mus_musculusAGGCAGAAES 10pg Nxt 703 503N128141,61297.4816,542,27214.37100.000.0093.7636.28
112815Mus_musculusTCCTGAGCST 1-1 Nxt 704 504N128151,98497.5220,342,05817.67100.000.0092.7035.86
112816Mus_musculusGGACTCCTES 1-1 Nxt 705 503N128161,35896.1714,116,36812.27100.000.0092.4435.87
112817Mus_musculusTAGGCATGES 1-2 Nxt 706 504N128171,82097.4518,681,38116.23100.000.0093.8436.31
1lane1unknownUndeterminedClusters with unmatched barcodes for lane 1NUndetermined_indices27265.774,129,3503.590.000.0089.4235.01
212754Mus_musculusAGGCAGAAIllumina index_N703_N502_Paired ends_LCMD250_Mm_CastaneusXC57Bl_PurkinjeN127541,58597.0016,340,81012.35100.000.0093.9136.35
212818Homo_sapiensCGTACTAGIllumina index_N702_N501_Paired ends_GM12878_200_singlecellN128181,59392.3617,246,98113.03100.000.0087.5534.39
212820Homo_sapiensTAGGCATGIllumina index_N706_N503_Paired ends_GM12878_208_singlecellN128202,20996.5422,878,84517.29100.000.0093.7536.26
212821Homo_sapiensTAAGGCGAIllumina index_N701_N501_Paired ends_GM12878_poolsplit_5_singlecellN128211,93593.0020,809,51215.73100.000.0088.8834.63
212822Homo_sapiensTCCTGAGCIllumina index_N704_N503_Paired ends_GM12878_poolsplit_6_singlecellN128222,98596.4930,936,67023.38100.000.0092.6835.77
2lane2unknownUndeterminedClusters with unmatched barcodes for lane 2NUndetermined_indices47919.8724,108,30218.220.000.0081.0032.24
312744Mus_musculusTAAGGCGAIllumina index_N701_N504_Paired ends_LCMD240_Mm_CastaneusXC57Bl_PurkinjeN127441,87596.8819,349,61615.49100.000.0094.0536.49
312749Mus_musculusTCCTGAGCIllumina index_N704_N502_Paired ends_LCMD245_Mm_CastaneusXC57Bl_PurkinjeN127491,73296.8917,878,21014.31100.000.0093.9836.43
312819Homo_sapiensGGACTCCTIllumina index_N705_N502_Paired ends_GM12878_205_singlecellN128191,97796.6520,460,06416.38100.000.0094.1936.48
312823Homo_sapiensCGTACTAGIllumina index_N702_N502_Paired ends_GM12878_poolsplit_7_singlecellN128231,96996.6720,364,12316.30100.000.0093.2936.16
312824Homo_sapiensAGGCAGAAIllumina index_N703_N504_Paired ends_GM12878_poolsplit_8_singlecellN128242,24596.9423,159,46618.54100.000.0093.3636.14
3lane3unknownUndeterminedClusters with unmatched barcodes for lane 3NUndetermined_indices1,91280.6023,724,89718.990.000.0082.4932.94
+

+

Sample information

+
+++++ + + + + + +
Sample

ID		RecipeOperatorDirectory
+
+++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
12812SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Project_12812/Sample_12812
12813SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Project_12813/Sample_12813
12814SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Project_12814/Sample_12814
12815SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Project_12815/Sample_12815
12816SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Project_12816/Sample_12816
12817SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Project_12817/Sample_12817
lane1SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Undetermined_indices/Sample_lane1
12754SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Project_12754/Sample_12754
12818SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Project_12818/Sample_12818
12820SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Project_12820/Sample_12820
12821SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Project_12821/Sample_12821
12822SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Project_12822/Sample_12822
lane2SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Undetermined_indices/Sample_lane2
12744SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Project_12744/Sample_12744
12749SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Project_12749/Sample_12749
12819SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Project_12819/Sample_12819
12823SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Project_12823/Sample_12823
12824SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Project_12824/Sample_12824
lane3SR_indexingLorian/mmjggl/jenner/rotifer/120406_SN787_0114_AD0PMDACXX/Unaligned_8ntIndex/Undetermined_indices/Sample_lane3
+

CASAVA-1.8.2

+ + diff --git a/htsworkflow/pipelines/test/testdata/1_12/basecall_stats/IVC.htm b/htsworkflow/pipelines/test/testdata/1_12/basecall_stats/IVC.htm new file mode 100644 index 0000000..3ffbe47 --- /dev/null +++ b/htsworkflow/pipelines/test/testdata/1_12/basecall_stats/IVC.htm @@ -0,0 +1,9 @@ + + + + +120406_SN787_0114_AD0PMDACXX IVC

120406_SN787_0114_AD0PMDACXX Intensity Plots

+ + + +
LaneAllCalled% Base Calls% All% Called
1
2
3
-- 2.30.2