From: Diane Trout Date: Wed, 3 Dec 2008 22:22:31 +0000 (+0000) Subject: Add code to create a paired end Summary.htm file X-Git-Tag: stanford.caltech-merged-database-2009-jan-15~19 X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=41d201f18f1324dd2dbad0c21b53325e642a65ad Add code to create a paired end Summary.htm file --- diff --git a/htsworkflow/pipelines/test/simulate_runfolder.py b/htsworkflow/pipelines/test/simulate_runfolder.py index f5e2c1e..f527a7b 100644 --- a/htsworkflow/pipelines/test/simulate_runfolder.py +++ b/htsworkflow/pipelines/test/simulate_runfolder.py @@ -4,7 +4,13 @@ Create simulated solexa/illumina runfolders for testing import os - +def make_firecrest_dir(data_dir, version="1.9.2", start=1, stop=37): + firecrest_dir = os.path.join(data_dir, + 'C%d-%d_Firecrest%s_12-04-2008_diane' % (start, stop, version) + ) + os.mkdir(firecrest_dir) + return firecrest_dir + def make_ipar_dir(data_dir): """ Construct an artificial ipar parameter file and directory @@ -819,6 +825,674 @@ def make_summary100_htm(gerald_dir): f.write(summary_htm) f.close() +def make_summary_paired_htm(gerald_dir): + summary_htm = """ + + + + +

080920_HWI-EAS229_0057_30GBJAAXX Summary

 +

Summary Information For Experiment 080920_HWI-EAS229_0057_30GBJAAXX on Machine unknown

+



Chip Summary

+ + + + +
MachineUNKNOWN
Run Folder080920_HWI-EAS229_0057_30GBJAAXX
Chip IDunknown
+



Chip Results Summary

+ + + + + + + + + + +
ClustersClusters (PF)Yield (kbases)
126151880959234563549167
+



Lane Parameter Summary

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
LaneSample IDSample TargetSample TypeLengthFilterNum TilesTiles
1unknownmm9ELAND_PAIR37, 37'((CHASTITY>=0.6))'100Lane 1
2unknownhg18ELAND_PAIR37, 37'((CHASTITY>=0.6))'100Lane 2
3unknownmm9ELAND_PAIR37, 37'((CHASTITY>=0.6))'100Lane 3
4unknownmm9ELAND_PAIR37, 37'((CHASTITY>=0.6))'100Lane 4
5unknownmm9ELAND_PAIR37, 37'((CHASTITY>=0.6))'100Lane 5
6unknownhg18ELAND_PAIR37, 37'((CHASTITY>=0.6))'100Lane 6
7unknownmm9ELAND_PAIR37, 37'((CHASTITY>=0.6))'100Lane 7
8unknownmm9ELAND_PAIR37, 37'((CHASTITY>=0.6))'100Lane 8
+



Lane Results Summary : Read 1

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Lane InfoTile Mean +/- SD for Lane
Lane Lane Yield (kbases) Clusters (raw)Clusters (PF) 1st Cycle Int (PF) % intensity after 20 cycles (PF) % PF Clusters % Align (PF) Alignment Score (PF) % Error Rate (PF)
1277083103646 +/- 451574887 +/- 6080290 +/- 1799.34 +/- 3.5272.22 +/- 4.6389.19 +/- 0.5914.16 +/- 0.630.94 +/- 0.17
2289563106678 +/- 465278260 +/- 2539294 +/- 1698.23 +/- 2.6673.43 +/- 2.5287.05 +/- 0.6416.81 +/- 0.550.92 +/- 0.17
325924284583 +/- 596370065 +/- 4194284 +/- 1899.82 +/- 3.0582.90 +/- 1.3289.49 +/- 0.2018.13 +/- 0.660.81 +/- 0.13
421054968813 +/- 478256905 +/- 4145300 +/- 29102.00 +/- 14.7482.91 +/- 5.8956.93 +/- 0.8225.85 +/- 2.300.95 +/- 0.30
5295555104854 +/- 466479879 +/- 6270281 +/- 1998.26 +/- 5.8576.34 +/- 6.6757.71 +/- 0.3026.16 +/- 1.680.97 +/- 0.19
614040143555 +/- 163237946 +/- 2140233 +/- 16105.74 +/- 8.4087.14 +/- 3.8789.08 +/- 1.0033.53 +/- 2.181.05 +/- 0.21
715421754265 +/- 158841680 +/- 5319224 +/- 18111.33 +/- 8.9076.94 +/- 10.5284.50 +/- 1.4127.44 +/- 2.331.32 +/- 0.25
814796964363 +/- 269739991 +/- 6785248 +/- 43109.93 +/- 7.8062.45 +/- 12.0582.20 +/- 2.0824.63 +/- 2.531.57 +/- 0.22
Tile mean across chip
Av.7884459952269103.0876.7979.5223.341.06
+



Lane Results Summary : Read 2

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Lane InfoTile Mean +/- SD for Lane
Lane Lane Yield (kbases) Clusters (raw)Clusters (PF) 1st Cycle Int (PF) % intensity after 20 cycles (PF) % PF Clusters % Align (PF) Alignment Score (PF) % Error Rate (PF)
1277083103646 +/- 451574887 +/- 6080277 +/- 1794.42 +/- 5.6872.22 +/- 4.6381.54 +/- 2.1342.70 +/- 5.490.89 +/- 0.27
2289563106678 +/- 465278260 +/- 2539259 +/- 1393.57 +/- 2.5573.43 +/- 2.5282.05 +/- 0.3743.98 +/- 3.020.76 +/- 0.15
325924284583 +/- 596370065 +/- 4194252 +/- 1294.23 +/- 2.1982.90 +/- 1.3284.94 +/- 0.2851.76 +/- 2.290.59 +/- 0.07
421054968813 +/- 478256905 +/- 4145226 +/- 1696.82 +/- 7.1282.91 +/- 5.8956.01 +/- 0.9927.86 +/- 3.480.95 +/- 0.33
5295555104854 +/- 466479879 +/- 6270200 +/- 24103.56 +/- 15.4576.34 +/- 6.6756.76 +/- 0.4125.68 +/- 2.060.98 +/- 0.17
614040143555 +/- 163237946 +/- 2140179 +/- 10100.82 +/- 5.4787.14 +/- 3.8788.64 +/- 1.4234.05 +/- 2.600.98 +/- 0.22
715421754265 +/- 158841680 +/- 5319184 +/- 5103.42 +/- 3.4776.94 +/- 10.5283.90 +/- 1.3227.60 +/- 2.071.26 +/- 0.16
814796964363 +/- 269739991 +/- 6785206 +/- 3199.48 +/- 3.2362.45 +/- 12.0579.81 +/- 3.3523.06 +/- 2.501.56 +/- 0.23
Tile mean across chip
Av.788445995222398.2976.7976.7034.591.00
+



Expanded Lane Summary : Read 1

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Lane InfoPhasing InfoRaw Data (tile mean)Filtered Data (tile mean)
Lane Clusters (tile mean) (raw)% Phasing % Prephasing % Error Rate (raw) Equiv Perfect Clusters (raw) % retained Cycle 2-4 Av Int (PF) Cycle 2-10 Av % Loss (PF) Cycle 10-20 Av % Loss (PF) % Align (PF) % Error Rate (PF) Equiv Perfect Clusters (PF)
11036460.86000.49001.377481372.22266 +/- 17-0.53 +/- 0.37-0.42 +/- 0.2189.190.9464718
21066780.86000.49001.347484273.43284 +/- 160.08 +/- 0.43-0.17 +/- 0.3487.050.9265850
3845830.86000.49001.096549382.90286 +/- 140.29 +/- 0.48-0.02 +/- 0.1789.490.8160899
4688130.86000.49001.193369782.91286 +/- 23-0.01 +/- 0.62-0.37 +/- 0.3056.930.9531080
51048540.86000.49001.325007576.34258 +/- 25-0.03 +/- 0.46-0.49 +/- 0.2757.710.9744149
6435550.86000.49001.243439987.14231 +/- 14-0.19 +/- 0.46-0.34 +/- 0.4089.081.0532302
7542650.86000.49001.673818876.94224 +/- 14-0.41 +/- 0.49-0.55 +/- 0.2384.501.3233435
8643630.86000.49002.153807762.45247 +/- 42-0.52 +/- 0.36-0.29 +/- 0.1982.201.5731036
+



Expanded Lane Summary : Read 2

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Lane InfoPhasing InfoRaw Data (tile mean)Filtered Data (tile mean)
Lane Clusters (tile mean) (raw)% Phasing % Prephasing % Error Rate (raw) Equiv Perfect Clusters (raw) % retained Cycle 2-4 Av Int (PF) Cycle 2-10 Av % Loss (PF) Cycle 10-20 Av % Loss (PF) % Align (PF) % Error Rate (PF) Equiv Perfect Clusters (PF)
11036460.79000.46001.246887072.22254 +/- 15-0.53 +/- 0.37-0.42 +/- 0.2181.540.8959272
21066780.79000.46001.117198073.43247 +/- 120.08 +/- 0.43-0.17 +/- 0.3482.050.7662240
3845830.79000.46000.806350082.90243 +/- 80.29 +/- 0.48-0.02 +/- 0.1784.940.5958029
4688130.79000.46001.123353482.91210 +/- 19-0.01 +/- 0.62-0.37 +/- 0.3056.010.9530548
51048540.79000.46001.244995176.34193 +/- 12-0.03 +/- 0.46-0.49 +/- 0.2756.760.9843366
6435550.79000.46001.123475187.14174 +/- 7-0.19 +/- 0.46-0.34 +/- 0.4088.640.9832208
7542650.79000.46001.553841876.94178 +/- 4-0.41 +/- 0.49-0.55 +/- 0.2383.901.2633240
8643630.79000.46002.073696862.45198 +/- 32-0.52 +/- 0.36-0.29 +/- 0.1979.811.5630181
+ +""" + pathname = os.path.join(gerald_dir, 'Summary.htm') + f = open(pathname, 'w') + f.write(summary_htm) + f.close() + def make_eland_results(gerald_dir): eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759 ACATAGNCACAGACATAAACATAGACATAGAC U0 1 1 3 chrUextra.fa 28189829 R D. >HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 chr2L.fa 8796855 R DD 24T