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Test 1.1rc1 style runs, which unfortunately require a hack for parsing
[htsworkflow.git] / htsworkflow / pipelines / test / simulate_runfolder.py
diff --git a/htsworkflow/pipelines/test/simulate_runfolder.py b/htsworkflow/pipelines/test/simulate_runfolder.py
index f527a7b086fcdae31ed8f068cf5c80e5cb4b7ce4..112201a281f6e46369eda926484480e2b17b5d7d 100644 (file)
--- a/htsworkflow/pipelines/test/simulate_runfolder.py
+++ b/htsworkflow/pipelines/test/simulate_runfolder.py
@@ -825,6 +825,412 @@ def make_summary100_htm(gerald_dir):
     f.write(summary_htm)
     f.close()
 
+def make_summary_htm_110(gerald_dir):
+    summary_htm = """<!--RUN_TIME Tue Oct 28 09:45:50 2008 -->
+<!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.10 2008/07/23 15:18:30 mzerara Exp $-->
+<html>
+<body>
+
+<a name="Top"><h2><title>081017_HWI-EAS229_0062_30J55AAXX Summary</title></h2></a>
+<h1>Summary Information For Experiment 081017_HWI-EAS229_0062_30J55AAXX on Machine HWI-EAS229</h1>
+<h2><br></br>Chip Summary<br></br></h2>
+<table border="1" cellpadding="5">
+<tr><td>Machine</td><td>HWI-EAS229</td></tr>
+<tr><td>Run Folder</td><td>081017_HWI-EAS229_0062_30J55AAXX</td></tr>
+<tr><td>Chip ID</td><td>unknown</td></tr>
+</table>
+<h2><br></br>Chip Results Summary<br></br></h2>
+<table border="1" cellpadding="5">
+<tr>
+<td>Clusters</td>
+<td>Clusters (PF)</td>
+<td>Yield (kbases)</td>
+</tr>
+<tr><td>162491175</td>
+<td>99622159</td>
+<td>3686019</td>
+</tr>
+</table>
+<h2><br></br>Lane Parameter Summary<br></br></h2>
+<table border="1" cellpadding="5">
+<tr>
+<td>Lane</td>
+<td>Sample ID</td>
+<td>Sample Target</td>
+<td>Sample Type</td>
+<td>Length</td>
+<td>Filter</td>
+<td>Chast. Thresh.</td>
+<td>Num Tiles</td>
+<td>Tiles</td>
+</tr>
+<tr>
+<td>1</td>
+<td>unknown</td>
+<td>mm9</td>
+<td>ELAND</td>
+<td>37</td>
+<td>'((FAILED_CHASTITY<=1))'</td>
+<td>0.6</td>
+<td>100</td>
+<td><a href="#Lane1">Lane 1</a></td>
+</tr>
+<tr>
+<td>2</td>
+<td>unknown</td>
+<td>mm9</td>
+<td>ELAND</td>
+<td>37</td>
+<td>'((FAILED_CHASTITY<=1))'</td>
+<td>0.6</td>
+<td>100</td>
+<td><a href="#Lane2">Lane 2</a></td>
+</tr>
+<tr>
+<td>3</td>
+<td>unknown</td>
+<td>mm9</td>
+<td>ELAND</td>
+<td>37</td>
+<td>'((FAILED_CHASTITY<=1))'</td>
+<td>0.6</td>
+<td>100</td>
+<td><a href="#Lane3">Lane 3</a></td>
+</tr>
+<tr>
+<td>4</td>
+<td>unknown</td>
+<td>hg18</td>
+<td>ELAND</td>
+<td>37</td>
+<td>'((FAILED_CHASTITY<=1))'</td>
+<td>0.6</td>
+<td>100</td>
+<td><a href="#Lane4">Lane 4</a></td>
+</tr>
+<tr>
+<td>5</td>
+<td>unknown</td>
+<td>hg18</td>
+<td>ELAND</td>
+<td>37</td>
+<td>'((FAILED_CHASTITY<=1))'</td>
+<td>0.6</td>
+<td>100</td>
+<td><a href="#Lane5">Lane 5</a></td>
+</tr>
+<tr>
+<td>6</td>
+<td>unknown</td>
+<td>mm9</td>
+<td>ELAND</td>
+<td>37</td>
+<td>'((FAILED_CHASTITY<=1))'</td>
+<td>0.6</td>
+<td>100</td>
+<td><a href="#Lane6">Lane 6</a></td>
+</tr>
+<tr>
+<td>7</td>
+<td>unknown</td>
+<td>mm9</td>
+<td>ELAND</td>
+<td>37</td>
+<td>'((FAILED_CHASTITY<=1))'</td>
+<td>0.6</td>
+<td>100</td>
+<td><a href="#Lane7">Lane 7</a></td>
+</tr>
+<tr>
+<td>8</td>
+<td>unknown</td>
+<td>mm9</td>
+<td>ELAND</td>
+<td>37</td>
+<td>'((FAILED_CHASTITY<=1))'</td>
+<td>0.6</td>
+<td>100</td>
+<td><a href="#Lane8">Lane 8</a></td>
+</tr>
+</table>
+<h2><br></br>Lane Results Summary<br></br></h2>
+<table border="1" cellpadding="5">
+<tr>
+<td colspan="2">Lane Info</td>
+<td colspan="8">Tile Mean +/- SD for Lane</td>
+</tr>
+<tr>
+<td>Lane </td>
+<td>Lane Yield (kbases) </td>
+<td>Clusters (raw)</td>
+<td>Clusters (PF) </td>
+<td>1st Cycle Int (PF) </td>
+<td>% intensity after 20 cycles (PF) </td>
+<td>% PF Clusters </td>
+<td>% Align (PF) </td>
+<td>Alignment Score (PF) </td>
+<td> % Error Rate (PF) </td>
+</tr>
+<tr>
+<td>1</td>
+<td>435340</td>
+<td>190220 +/- 15118</td>
+<td>117659 +/- 8144</td>
+<td>273 +/- 16</td>
+<td>80.02 +/- 2.52</td>
+<td>62.15 +/- 5.54</td>
+<td>77.18 +/- 0.22</td>
+<td>13447.28 +/- 43.35</td>
+<td>2.78 +/- 0.13</td>
+</tr>
+<tr>
+<td>2</td>
+<td>462364</td>
+<td>190560 +/- 14399</td>
+<td>124963 +/- 5687</td>
+<td>271 +/- 16</td>
+<td>75.73 +/- 2.46</td>
+<td>65.83 +/- 4.12</td>
+<td>70.06 +/- 0.39</td>
+<td>12082.95 +/- 64.81</td>
+<td>3.22 +/- 0.09</td>
+</tr>
+<tr>
+<td>3</td>
+<td>468929</td>
+<td>187597 +/- 12369</td>
+<td>126737 +/- 5549</td>
+<td>274 +/- 16</td>
+<td>72.61 +/- 2.67</td>
+<td>67.69 +/- 2.72</td>
+<td>74.03 +/- 0.22</td>
+<td>12470.18 +/- 50.02</td>
+<td>4.27 +/- 0.08</td>
+</tr>
+<tr>
+<td>4</td>
+<td>491642</td>
+<td>204142 +/- 16877</td>
+<td>132876 +/- 4023</td>
+<td>253 +/- 16</td>
+<td>80.43 +/- 3.10</td>
+<td>65.39 +/- 3.84</td>
+<td>72.95 +/- 0.15</td>
+<td>13273.80 +/- 39.75</td>
+<td>0.78 +/- 0.10</td>
+</tr>
+<tr>
+<td>5</td>
+<td>433033</td>
+<td>247308 +/- 11600</td>
+<td>117036 +/- 4489</td>
+<td>273 +/- 11</td>
+<td>68.60 +/- 2.40</td>
+<td>47.48 +/- 3.63</td>
+<td>66.91 +/- 0.54</td>
+<td>11700.08 +/- 66.33</td>
+<td>2.62 +/- 0.13</td>
+</tr>
+<tr>
+<td>6</td>
+<td>483012</td>
+<td>204298 +/- 15640</td>
+<td>130543 +/- 6972</td>
+<td>254 +/- 11</td>
+<td>81.35 +/- 1.96</td>
+<td>64.14 +/- 4.40</td>
+<td>77.28 +/- 0.11</td>
+<td>14084.01 +/- 23.09</td>
+<td>0.71 +/- 0.03</td>
+</tr>
+<tr>
+<td>7</td>
+<td>474325</td>
+<td>202707 +/- 15404</td>
+<td>128196 +/- 9745</td>
+<td>255 +/- 13</td>
+<td>79.95 +/- 2.08</td>
+<td>63.48 +/- 5.63</td>
+<td>75.78 +/- 0.18</td>
+<td>13758.74 +/- 60.86</td>
+<td>0.88 +/- 0.12</td>
+</tr>
+<tr>
+<td>8</td>
+<td>437372</td>
+<td>198075 +/- 14702</td>
+<td>118208 +/- 14798</td>
+<td>259 +/- 14</td>
+<td>81.80 +/- 2.53</td>
+<td>59.85 +/- 7.67</td>
+<td>74.55 +/- 0.36</td>
+<td>13586.07 +/- 103.97</td>
+<td>0.71 +/- 0.15</td>
+</tr>
+<tr><td colspan="13">Tile mean across chip</td></tr>
+<tr>
+<td>Av.</td>
+<td></td>
+<td>203113</td>
+<td>124527</td>
+<td>264</td>
+<td>77.56</td>
+<td>62.00</td>
+<td>73.59</td>
+<td>13050.39</td>
+<td>2.00</td>
+</tr>
+</table>
+<h2><br></br>Expanded Lane Summary<br></br></h2>
+<table border="1" cellpadding="5">
+<tr>
+
+<tr><td colspan="2">Lane Info</td>
+<td colspan="2">Phasing Info</td>
+<td colspan="2">Raw Data (tile mean)</td>
+<td colspan="7">Filtered Data (tile mean)</td></tr>
+<td>Lane </td>
+<td>Clusters (tile mean) (raw)</td>
+<td>% Phasing </td>
+<td>% Prephasing </td>
+<td>% Error Rate (raw) </td>
+<td> Equiv Perfect Clusters (raw) </td>
+<td>% retained </td>
+<td>Cycle 2-4 Av Int (PF) </td>
+<td>Cycle 2-10 Av % Loss (PF) </td>
+<td>Cycle 10-20 Av % Loss (PF) </td>
+<td>% Align (PF) </td>
+<td>% Error Rate (PF) </td>
+<td> Equiv Perfect Clusters (PF) </td>
+</tr>
+<tr>
+<td>1</td>
+<td>190220</td>
+<td>0.6800</td>
+<td>0.2800</td>
+<td>3.17</td>
+<td>107262</td>
+<td>62.15</td>
+<td>241 +/- 13</td>
+<td>0.56 +/- 0.22</td>
+<td>0.29 +/- 0.14</td>
+<td>77.18</td>
+<td>2.78</td>
+<td>86184</td>
+</tr>
+<tr>
+<td>2</td>
+<td>190560</td>
+<td>0.6800</td>
+<td>0.2800</td>
+<td>3.53</td>
+<td>98678</td>
+<td>65.83</td>
+<td>238 +/- 14</td>
+<td>0.78 +/- 0.15</td>
+<td>0.53 +/- 0.15</td>
+<td>70.06</td>
+<td>3.22</td>
+<td>83090</td>
+</tr>
+<tr>
+<td>3</td>
+<td>187597</td>
+<td>0.6800</td>
+<td>0.2800</td>
+<td>4.44</td>
+<td>104008</td>
+<td>67.69</td>
+<td>233 +/- 14</td>
+<td>0.56 +/- 0.17</td>
+<td>0.59 +/- 0.26</td>
+<td>74.03</td>
+<td>4.27</td>
+<td>89278</td>
+</tr>
+<tr>
+<td>4</td>
+<td>204142</td>
+<td>0.6800</td>
+<td>0.2800</td>
+<td>1.38</td>
+<td>115765</td>
+<td>65.39</td>
+<td>239 +/- 14</td>
+<td>1.28 +/- 0.21</td>
+<td>0.77 +/- 0.21</td>
+<td>72.95</td>
+<td>0.78</td>
+<td>93475</td>
+</tr>
+<tr>
+<td>5</td>
+<td>247308</td>
+<td>0.6800</td>
+<td>0.2800</td>
+<td>3.40</td>
+<td>103006</td>
+<td>47.48</td>
+<td>242 +/- 10</td>
+<td>1.61 +/- 0.39</td>
+<td>1.21 +/- 0.21</td>
+<td>66.91</td>
+<td>2.62</td>
+<td>73768</td>
+</tr>
+<tr>
+<td>6</td>
+<td>204298</td>
+<td>0.6800</td>
+<td>0.2800</td>
+<td>1.33</td>
+<td>122233</td>
+<td>64.14</td>
+<td>242 +/- 12</td>
+<td>1.30 +/- 0.11</td>
+<td>0.73 +/- 0.22</td>
+<td>77.28</td>
+<td>0.71</td>
+<td>97646</td>
+</tr>
+<tr>
+<td>7</td>
+<td>202707</td>
+<td>0.6800</td>
+<td>0.2800</td>
+<td>1.51</td>
+<td>117513</td>
+<td>63.48</td>
+<td>238 +/- 13</td>
+<td>1.27 +/- 0.38</td>
+<td>0.66 +/- 0.22</td>
+<td>75.78</td>
+<td>0.88</td>
+<td>93659</td>
+</tr>
+<tr>
+<td>8</td>
+<td>198075</td>
+<td>0.6800</td>
+<td>0.2800</td>
+<td>1.41</td>
+<td>111115</td>
+<td>59.85</td>
+<td>244 +/- 12</td>
+<td>1.19 +/- 0.16</td>
+<td>0.65 +/- 0.29</td>
+<td>74.55</td>
+<td>0.71</td>
+<td>85327</td>
+</tr>
+</table>
+</body>
+</html>"""
+    pathname = os.path.join(gerald_dir, 'Summary.htm')
+    f = open(pathname, 'w')
+    f.write(summary_htm)
+    f.close()
+
 def make_summary_paired_htm(gerald_dir):
     summary_htm = """<!--RUN_TIME Thu Nov 13 15:11:29 2008 -->
 <!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.94 2007/12/04 09:59:07 rshaw Exp $-->
htsworkflow sequencing LIMS software