replace example output

roblanf · May 28, 2018 · dc3afdf · dc3afdf
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diff --git a/example_output/RB7_A2/MinIONQC/.flowcell_overview.png-F4H4 b/example_output/RB7_A2/MinIONQC/.flowcell_overview.png-F4H4
diff --git a/example_output/RB7_A2/MinIONQC/channel_summary.png b/example_output/RB7_A2/MinIONQC/channel_summary.png
diff --git a/example_output/RB7_A2/MinIONQC/flowcell_overview.png b/example_output/RB7_A2/MinIONQC/flowcell_overview.png
diff --git a/example_output/RB7_A2/MinIONQC/length_by_hour.png b/example_output/RB7_A2/MinIONQC/length_by_hour.png
diff --git a/example_output/RB7_A2/MinIONQC/length_histogram.png b/example_output/RB7_A2/MinIONQC/length_histogram.png
diff --git a/example_output/RB7_A2/MinIONQC/length_vs_q.png b/example_output/RB7_A2/MinIONQC/length_vs_q.png
diff --git a/example_output/RB7_A2/MinIONQC/q_by_hour.png b/example_output/RB7_A2/MinIONQC/q_by_hour.png
diff --git a/example_output/RB7_A2/MinIONQC/q_histogram.png b/example_output/RB7_A2/MinIONQC/q_histogram.png
diff --git a/example_output/RB7_A2/MinIONQC/reads_per_hour.png b/example_output/RB7_A2/MinIONQC/reads_per_hour.png
diff --git a/example_output/RB7_A2/MinIONQC/summary.yaml b/example_output/RB7_A2/MinIONQC/summary.yaml
@@ -0,0 +1,57 @@
+input file: /Users/roblanfear/Desktop/example_input/RB7_A2/sequencing_summary.txt
+All reads:
+  total.gigabases: 3.527993
+  total.reads: 238421
+  N50.length: 34625.0
+  mean.length: 14797.3
+  median.length: 5852.0
+  max.length: 208407.0
+  mean.q: 7.9
+  median.q: 9.0
+  reads:
+    '>10kb': 108102
+    '>20kb': 80309
+    '>50kb': 13325
+    '>100kb': 181
+    '>200kb': 1
+    '>500kb': 0
+    '>1m': 0
+    ultralong: 390.0
+  gigabases:
+    '>10kb': 3.3802968
+    '>20kb': 2.949691
+    '>50kb': 0.8406423
+    '>100kb': 0.0199968
+    '>200kb': 0.0002084
+    '>500kb': 0.0e+00
+    '>1m': 0.0e+00
+    ultralong: 0.0399325
+Q>=7:
+  total.gigabases: 3.4512843
+  total.reads: 131847
+  N50.length: 34965.0
+  mean.length: 26176.4
+  median.length: 23673.0
+  max.length: 208407.0
+  mean.q: 10.9
+  median.q: 11.2
+  reads:
+    '>10kb': 105306
+    '>20kb': 79150
+    '>50kb': 13274
+    '>100kb': 180
+    '>200kb': 1
+    '>500kb': 0
+    '>1m': 0
+    ultralong: 388.0
+  gigabases:
+    '>10kb': 3.3211363
+    '>20kb': 2.9143651
+    '>50kb': 0.8375402
+    '>100kb': 0.0198897
+    '>200kb': 0.0002084
+    '>500kb': 0.0e+00
+    '>1m': 0.0e+00
+    ultralong: 0.0397338
+notes: ultralong reads refers to the largest set of reads with N50>100KB
+
diff --git a/example_output/RB7_A2/MinIONQC/yield_by_length.png b/example_output/RB7_A2/MinIONQC/yield_by_length.png
diff --git a/example_output/RB7_A2/MinIONQC/yield_over_time.png b/example_output/RB7_A2/MinIONQC/yield_over_time.png
diff --git a/example_output/RB7_D3/MinIONQC/channel_summary.png b/example_output/RB7_D3/MinIONQC/channel_summary.png
diff --git a/example_output/RB7_D3/MinIONQC/flowcell_overview.png b/example_output/RB7_D3/MinIONQC/flowcell_overview.png
diff --git a/example_output/RB7_D3/MinIONQC/length_by_hour.png b/example_output/RB7_D3/MinIONQC/length_by_hour.png
diff --git a/example_output/RB7_D3/MinIONQC/length_histogram.png b/example_output/RB7_D3/MinIONQC/length_histogram.png
diff --git a/example_output/RB7_D3/MinIONQC/length_vs_q.png b/example_output/RB7_D3/MinIONQC/length_vs_q.png
diff --git a/example_output/RB7_D3/MinIONQC/q_by_hour.png b/example_output/RB7_D3/MinIONQC/q_by_hour.png
diff --git a/example_output/RB7_D3/MinIONQC/q_histogram.png b/example_output/RB7_D3/MinIONQC/q_histogram.png
diff --git a/example_output/RB7_D3/MinIONQC/reads_per_hour.png b/example_output/RB7_D3/MinIONQC/reads_per_hour.png
diff --git a/example_output/RB7_D3/MinIONQC/summary.yaml b/example_output/RB7_D3/MinIONQC/summary.yaml
@@ -0,0 +1,57 @@
+input file: /Users/roblanfear/Desktop/example_input/RB7_D3/sequencing_summary.txt
+All reads:
+  total.gigabases: 3.6753083
+  total.reads: 369787
+  N50.length: 31587.0
+  mean.length: 9939.0
+  median.length: 1802.0
+  max.length: 494586.0
+  mean.q: 7.3
+  median.q: 7.0
+  reads:
+    '>10kb': 114575
+    '>20kb': 72409
+    '>50kb': 11970
+    '>100kb': 145
+    '>200kb': 1
+    '>500kb': 0
+    '>1m': 0
+    ultralong: 319.0
+  gigabases:
+    '>10kb': 3.286376
+    '>20kb': 2.6701066
+    '>50kb': 0.747287
+    '>100kb': 0.0165945
+    '>200kb': 0.0004946
+    '>500kb': 0.0e+00
+    '>1m': 0.0e+00
+    ultralong: 0.0331235
+Q>=7:
+  total.gigabases: 3.5474855
+  total.reads: 184499
+  N50.length: 32202.0
+  mean.length: 19227.7
+  median.length: 14077.0
+  max.length: 153159.0
+  mean.q: 10.6
+  median.q: 10.8
+  reads:
+    '>10kb': 110607
+    '>20kb': 70757
+    '>50kb': 11889
+    '>100kb': 143
+    '>200kb': 0
+    '>500kb': 0
+    '>1m': 0
+    ultralong: 310.0
+  gigabases:
+    '>10kb': 3.2036826
+    '>20kb': 2.6201044
+    '>50kb': 0.74202
+    '>100kb': 0.0159276
+    '>200kb': 0.0e+00
+    '>500kb': 0.0e+00
+    '>1m': 0.0e+00
+    ultralong: 0.0318148
+notes: ultralong reads refers to the largest set of reads with N50>100KB
+
diff --git a/example_output/RB7_D3/MinIONQC/yield_by_length.png b/example_output/RB7_D3/MinIONQC/yield_by_length.png
diff --git a/example_output/RB7_D3/MinIONQC/yield_over_time.png b/example_output/RB7_D3/MinIONQC/yield_over_time.png
diff --git a/example_output/combinedQC/combined_length_histogram.png b/example_output/combinedQC/combined_length_histogram.png
diff --git a/example_output/combinedQC/combined_q_histogram.png b/example_output/combinedQC/combined_q_histogram.png
diff --git a/example_output/combinedQC/combined_yield_by_length.png b/example_output/combinedQC/combined_yield_by_length.png
diff --git a/example_output/combinedQC/length_by_hour.png b/example_output/combinedQC/length_by_hour.png
diff --git a/example_output/combinedQC/length_distributions.png b/example_output/combinedQC/length_distributions.png
diff --git a/example_output/combinedQC/q_by_hour.png b/example_output/combinedQC/q_by_hour.png
diff --git a/example_output/combinedQC/q_distributions.png b/example_output/combinedQC/q_distributions.png
diff --git a/example_output/combinedQC/summary.yaml b/example_output/combinedQC/summary.yaml
@@ -0,0 +1,57 @@
+input file: /Users/roblanfear/Desktop/example_input
+All reads:
+  total.gigabases: 7.2033013
+  total.reads: 608208
+  N50.length: 33161.0
+  mean.length: 11843.5
+  median.length: 2555.0
+  max.length: 494586.0
+  mean.q: 7.5
+  median.q: 7.7
+  reads:
+    '>10kb': 222677
+    '>20kb': 152718
+    '>50kb': 25295
+    '>100kb': 326
+    '>200kb': 2
+    '>500kb': 0
+    '>1m': 0
+    ultralong: 710.0
+  gigabases:
+    '>10kb': 6.6666729
+    '>20kb': 5.6197975
+    '>50kb': 1.5879293
+    '>100kb': 0.0365913
+    '>200kb': 0.000703
+    '>500kb': 0.0e+00
+    '>1m': 0.0e+00
+    ultralong: 0.0731478
+Q>=7:
+  total.gigabases: 6.9987697
+  total.reads: 316346
+  N50.length: 33638.0
+  mean.length: 22123.8
+  median.length: 18795.5
+  max.length: 208407.0
+  mean.q: 10.7
+  median.q: 11.0
+  reads:
+    '>10kb': 215913
+    '>20kb': 149907
+    '>50kb': 25163
+    '>100kb': 323
+    '>200kb': 1
+    '>500kb': 0
+    '>1m': 0
+    ultralong: 698.0
+  gigabases:
+    '>10kb': 6.5248189
+    '>20kb': 5.5344695
+    '>50kb': 1.5795601
+    '>100kb': 0.0358173
+    '>200kb': 0.0002084
+    '>500kb': 0.0e+00
+    '>1m': 0.0e+00
+    ultralong: 0.0715487
+notes: ultralong reads refers to the largest set of reads with N50>100KB
+
diff --git a/example_output/combinedQC/yield_by_length.png b/example_output/combinedQC/yield_by_length.png
diff --git a/example_output/combinedQC/yield_over_time.png b/example_output/combinedQC/yield_over_time.png