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
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 $-->
+<html>
+<body>
+
+<a name="Top"><h2><title>080920_HWI-EAS229_0057_30GBJAAXX Summary</title></h2></a>
+<h1>Summary Information For Experiment 080920_HWI-EAS229_0057_30GBJAAXX on Machine unknown</h1>
+<h2><br></br>Chip Summary<br></br></h2>
+<table border="1" cellpadding="5">
+<tr><td>Machine</td><td>UNKNOWN</td></tr>
+<tr><td>Run Folder</td><td>080920_HWI-EAS229_0057_30GBJAAXX</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>126151880</td>
+<td>95923456</td>
+<td>3549167</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>Num Tiles</td>
+<td>Tiles</td>
+</tr>
+<tr>
+<td>1</td>
+<td>unknown</td>
+<td>mm9</td>
+<td>ELAND_PAIR</td>
+<td>37, 37</td>
+<td>'((CHASTITY>=0.6))'</td>
+<td>100</td>
+<td><a href="#Lane1">Lane 1</a></td>
+</tr>
+<tr>
+<td>2</td>
+<td>unknown</td>
+<td>hg18</td>
+<td>ELAND_PAIR</td>
+<td>37, 37</td>
+<td>'((CHASTITY>=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_PAIR</td>
+<td>37, 37</td>
+<td>'((CHASTITY>=0.6))'</td>
+<td>100</td>
+<td><a href="#Lane3">Lane 3</a></td>
+</tr>
+<tr>
+<td>4</td>
+<td>unknown</td>
+<td>mm9</td>
+<td>ELAND_PAIR</td>
+<td>37, 37</td>
+<td>'((CHASTITY>=0.6))'</td>
+<td>100</td>
+<td><a href="#Lane4">Lane 4</a></td>
+</tr>
+<tr>
+<td>5</td>
+<td>unknown</td>
+<td>mm9</td>
+<td>ELAND_PAIR</td>
+<td>37, 37</td>
+<td>'((CHASTITY>=0.6))'</td>
+<td>100</td>
+<td><a href="#Lane5">Lane 5</a></td>
+</tr>
+<tr>
+<td>6</td>
+<td>unknown</td>
+<td>hg18</td>
+<td>ELAND_PAIR</td>
+<td>37, 37</td>
+<td>'((CHASTITY>=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_PAIR</td>
+<td>37, 37</td>
+<td>'((CHASTITY>=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_PAIR</td>
+<td>37, 37</td>
+<td>'((CHASTITY>=0.6))'</td>
+<td>100</td>
+<td><a href="#Lane8">Lane 8</a></td>
+</tr>
+</table>
+<h2><br></br>Lane Results Summary : Read 1<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>277083</td>
+<td>103646 +/- 4515</td>
+<td>74887 +/- 6080</td>
+<td>290 +/- 17</td>
+<td>99.34 +/- 3.52</td>
+<td>72.22 +/- 4.63</td>
+<td>89.19 +/- 0.59</td>
+<td>14.16 +/- 0.63</td>
+<td>0.94 +/- 0.17</td>
+</tr>
+<tr>
+<td>2</td>
+<td>289563</td>
+<td>106678 +/- 4652</td>
+<td>78260 +/- 2539</td>
+<td>294 +/- 16</td>
+<td>98.23 +/- 2.66</td>
+<td>73.43 +/- 2.52</td>
+<td>87.05 +/- 0.64</td>
+<td>16.81 +/- 0.55</td>
+<td>0.92 +/- 0.17</td>
+</tr>
+<tr>
+<td>3</td>
+<td>259242</td>
+<td>84583 +/- 5963</td>
+<td>70065 +/- 4194</td>
+<td>284 +/- 18</td>
+<td>99.82 +/- 3.05</td>
+<td>82.90 +/- 1.32</td>
+<td>89.49 +/- 0.20</td>
+<td>18.13 +/- 0.66</td>
+<td>0.81 +/- 0.13</td>
+</tr>
+<tr>
+<td>4</td>
+<td>210549</td>
+<td>68813 +/- 4782</td>
+<td>56905 +/- 4145</td>
+<td>300 +/- 29</td>
+<td>102.00 +/- 14.74</td>
+<td>82.91 +/- 5.89</td>
+<td>56.93 +/- 0.82</td>
+<td>25.85 +/- 2.30</td>
+<td>0.95 +/- 0.30</td>
+</tr>
+<tr>
+<td>5</td>
+<td>295555</td>
+<td>104854 +/- 4664</td>
+<td>79879 +/- 6270</td>
+<td>281 +/- 19</td>
+<td>98.26 +/- 5.85</td>
+<td>76.34 +/- 6.67</td>
+<td>57.71 +/- 0.30</td>
+<td>26.16 +/- 1.68</td>
+<td>0.97 +/- 0.19</td>
+</tr>
+<tr>
+<td>6</td>
+<td>140401</td>
+<td>43555 +/- 1632</td>
+<td>37946 +/- 2140</td>
+<td>233 +/- 16</td>
+<td>105.74 +/- 8.40</td>
+<td>87.14 +/- 3.87</td>
+<td>89.08 +/- 1.00</td>
+<td>33.53 +/- 2.18</td>
+<td>1.05 +/- 0.21</td>
+</tr>
+<tr>
+<td>7</td>
+<td>154217</td>
+<td>54265 +/- 1588</td>
+<td>41680 +/- 5319</td>
+<td>224 +/- 18</td>
+<td>111.33 +/- 8.90</td>
+<td>76.94 +/- 10.52</td>
+<td>84.50 +/- 1.41</td>
+<td>27.44 +/- 2.33</td>
+<td>1.32 +/- 0.25</td>
+</tr>
+<tr>
+<td>8</td>
+<td>147969</td>
+<td>64363 +/- 2697</td>
+<td>39991 +/- 6785</td>
+<td>248 +/- 43</td>
+<td>109.93 +/- 7.80</td>
+<td>62.45 +/- 12.05</td>
+<td>82.20 +/- 2.08</td>
+<td>24.63 +/- 2.53</td>
+<td>1.57 +/- 0.22</td>
+</tr>
+<tr><td colspan="13">Tile mean across chip</td></tr>
+<tr>
+<td>Av.</td>
+<td></td>
+<td>78844</td>
+<td>59952</td>
+<td>269</td>
+<td>103.08</td>
+<td>76.79</td>
+<td>79.52</td>
+<td>23.34</td>
+<td>1.06</td>
+</tr>
+</table>
+<h2><br></br>Lane Results Summary : Read 2<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>277083</td>
+<td>103646 +/- 4515</td>
+<td>74887 +/- 6080</td>
+<td>277 +/- 17</td>
+<td>94.42 +/- 5.68</td>
+<td>72.22 +/- 4.63</td>
+<td>81.54 +/- 2.13</td>
+<td>42.70 +/- 5.49</td>
+<td>0.89 +/- 0.27</td>
+</tr>
+<tr>
+<td>2</td>
+<td>289563</td>
+<td>106678 +/- 4652</td>
+<td>78260 +/- 2539</td>
+<td>259 +/- 13</td>
+<td>93.57 +/- 2.55</td>
+<td>73.43 +/- 2.52</td>
+<td>82.05 +/- 0.37</td>
+<td>43.98 +/- 3.02</td>
+<td>0.76 +/- 0.15</td>
+</tr>
+<tr>
+<td>3</td>
+<td>259242</td>
+<td>84583 +/- 5963</td>
+<td>70065 +/- 4194</td>
+<td>252 +/- 12</td>
+<td>94.23 +/- 2.19</td>
+<td>82.90 +/- 1.32</td>
+<td>84.94 +/- 0.28</td>
+<td>51.76 +/- 2.29</td>
+<td>0.59 +/- 0.07</td>
+</tr>
+<tr>
+<td>4</td>
+<td>210549</td>
+<td>68813 +/- 4782</td>
+<td>56905 +/- 4145</td>
+<td>226 +/- 16</td>
+<td>96.82 +/- 7.12</td>
+<td>82.91 +/- 5.89</td>
+<td>56.01 +/- 0.99</td>
+<td>27.86 +/- 3.48</td>
+<td>0.95 +/- 0.33</td>
+</tr>
+<tr>
+<td>5</td>
+<td>295555</td>
+<td>104854 +/- 4664</td>
+<td>79879 +/- 6270</td>
+<td>200 +/- 24</td>
+<td>103.56 +/- 15.45</td>
+<td>76.34 +/- 6.67</td>
+<td>56.76 +/- 0.41</td>
+<td>25.68 +/- 2.06</td>
+<td>0.98 +/- 0.17</td>
+</tr>
+<tr>
+<td>6</td>
+<td>140401</td>
+<td>43555 +/- 1632</td>
+<td>37946 +/- 2140</td>
+<td>179 +/- 10</td>
+<td>100.82 +/- 5.47</td>
+<td>87.14 +/- 3.87</td>
+<td>88.64 +/- 1.42</td>
+<td>34.05 +/- 2.60</td>
+<td>0.98 +/- 0.22</td>
+</tr>
+<tr>
+<td>7</td>
+<td>154217</td>
+<td>54265 +/- 1588</td>
+<td>41680 +/- 5319</td>
+<td>184 +/- 5</td>
+<td>103.42 +/- 3.47</td>
+<td>76.94 +/- 10.52</td>
+<td>83.90 +/- 1.32</td>
+<td>27.60 +/- 2.07</td>
+<td>1.26 +/- 0.16</td>
+</tr>
+<tr>
+<td>8</td>
+<td>147969</td>
+<td>64363 +/- 2697</td>
+<td>39991 +/- 6785</td>
+<td>206 +/- 31</td>
+<td>99.48 +/- 3.23</td>
+<td>62.45 +/- 12.05</td>
+<td>79.81 +/- 3.35</td>
+<td>23.06 +/- 2.50</td>
+<td>1.56 +/- 0.23</td>
+</tr>
+<tr><td colspan="13">Tile mean across chip</td></tr>
+<tr>
+<td>Av.</td>
+<td></td>
+<td>78844</td>
+<td>59952</td>
+<td>223</td>
+<td>98.29</td>
+<td>76.79</td>
+<td>76.70</td>
+<td>34.59</td>
+<td>1.00</td>
+</tr>
+</table>
+<h2><br></br>Expanded Lane Summary : Read 1<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>103646</td>
+<td>0.8600</td>
+<td>0.4900</td>
+<td>1.37</td>
+<td>74813</td>
+<td>72.22</td>
+<td>266 +/- 17</td>
+<td>-0.53 +/- 0.37</td>
+<td>-0.42 +/- 0.21</td>
+<td>89.19</td>
+<td>0.94</td>
+<td>64718</td>
+</tr>
+<tr>
+<td>2</td>
+<td>106678</td>
+<td>0.8600</td>
+<td>0.4900</td>
+<td>1.34</td>
+<td>74842</td>
+<td>73.43</td>
+<td>284 +/- 16</td>
+<td>0.08 +/- 0.43</td>
+<td>-0.17 +/- 0.34</td>
+<td>87.05</td>
+<td>0.92</td>
+<td>65850</td>
+</tr>
+<tr>
+<td>3</td>
+<td>84583</td>
+<td>0.8600</td>
+<td>0.4900</td>
+<td>1.09</td>
+<td>65493</td>
+<td>82.90</td>
+<td>286 +/- 14</td>
+<td>0.29 +/- 0.48</td>
+<td>-0.02 +/- 0.17</td>
+<td>89.49</td>
+<td>0.81</td>
+<td>60899</td>
+</tr>
+<tr>
+<td>4</td>
+<td>68813</td>
+<td>0.8600</td>
+<td>0.4900</td>
+<td>1.19</td>
+<td>33697</td>
+<td>82.91</td>
+<td>286 +/- 23</td>
+<td>-0.01 +/- 0.62</td>
+<td>-0.37 +/- 0.30</td>
+<td>56.93</td>
+<td>0.95</td>
+<td>31080</td>
+</tr>
+<tr>
+<td>5</td>
+<td>104854</td>
+<td>0.8600</td>
+<td>0.4900</td>
+<td>1.32</td>
+<td>50075</td>
+<td>76.34</td>
+<td>258 +/- 25</td>
+<td>-0.03 +/- 0.46</td>
+<td>-0.49 +/- 0.27</td>
+<td>57.71</td>
+<td>0.97</td>
+<td>44149</td>
+</tr>
+<tr>
+<td>6</td>
+<td>43555</td>
+<td>0.8600</td>
+<td>0.4900</td>
+<td>1.24</td>
+<td>34399</td>
+<td>87.14</td>
+<td>231 +/- 14</td>
+<td>-0.19 +/- 0.46</td>
+<td>-0.34 +/- 0.40</td>
+<td>89.08</td>
+<td>1.05</td>
+<td>32302</td>
+</tr>
+<tr>
+<td>7</td>
+<td>54265</td>
+<td>0.8600</td>
+<td>0.4900</td>
+<td>1.67</td>
+<td>38188</td>
+<td>76.94</td>
+<td>224 +/- 14</td>
+<td>-0.41 +/- 0.49</td>
+<td>-0.55 +/- 0.23</td>
+<td>84.50</td>
+<td>1.32</td>
+<td>33435</td>
+</tr>
+<tr>
+<td>8</td>
+<td>64363</td>
+<td>0.8600</td>
+<td>0.4900</td>
+<td>2.15</td>
+<td>38077</td>
+<td>62.45</td>
+<td>247 +/- 42</td>
+<td>-0.52 +/- 0.36</td>
+<td>-0.29 +/- 0.19</td>
+<td>82.20</td>
+<td>1.57</td>
+<td>31036</td>
+</tr>
+</table>
+<h2><br></br>Expanded Lane Summary : Read 2<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>103646</td>
+<td>0.7900</td>
+<td>0.4600</td>
+<td>1.24</td>
+<td>68870</td>
+<td>72.22</td>
+<td>254 +/- 15</td>
+<td>-0.53 +/- 0.37</td>
+<td>-0.42 +/- 0.21</td>
+<td>81.54</td>
+<td>0.89</td>
+<td>59272</td>
+</tr>
+<tr>
+<td>2</td>
+<td>106678</td>
+<td>0.7900</td>
+<td>0.4600</td>
+<td>1.11</td>
+<td>71980</td>
+<td>73.43</td>
+<td>247 +/- 12</td>
+<td>0.08 +/- 0.43</td>
+<td>-0.17 +/- 0.34</td>
+<td>82.05</td>
+<td>0.76</td>
+<td>62240</td>
+</tr>
+<tr>
+<td>3</td>
+<td>84583</td>
+<td>0.7900</td>
+<td>0.4600</td>
+<td>0.80</td>
+<td>63500</td>
+<td>82.90</td>
+<td>243 +/- 8</td>
+<td>0.29 +/- 0.48</td>
+<td>-0.02 +/- 0.17</td>
+<td>84.94</td>
+<td>0.59</td>
+<td>58029</td>
+</tr>
+<tr>
+<td>4</td>
+<td>68813</td>
+<td>0.7900</td>
+<td>0.4600</td>
+<td>1.12</td>
+<td>33534</td>
+<td>82.91</td>
+<td>210 +/- 19</td>
+<td>-0.01 +/- 0.62</td>
+<td>-0.37 +/- 0.30</td>
+<td>56.01</td>
+<td>0.95</td>
+<td>30548</td>
+</tr>
+<tr>
+<td>5</td>
+<td>104854</td>
+<td>0.7900</td>
+<td>0.4600</td>
+<td>1.24</td>
+<td>49951</td>
+<td>76.34</td>
+<td>193 +/- 12</td>
+<td>-0.03 +/- 0.46</td>
+<td>-0.49 +/- 0.27</td>
+<td>56.76</td>
+<td>0.98</td>
+<td>43366</td>
+</tr>
+<tr>
+<td>6</td>
+<td>43555</td>
+<td>0.7900</td>
+<td>0.4600</td>
+<td>1.12</td>
+<td>34751</td>
+<td>87.14</td>
+<td>174 +/- 7</td>
+<td>-0.19 +/- 0.46</td>
+<td>-0.34 +/- 0.40</td>
+<td>88.64</td>
+<td>0.98</td>
+<td>32208</td>
+</tr>
+<tr>
+<td>7</td>
+<td>54265</td>
+<td>0.7900</td>
+<td>0.4600</td>
+<td>1.55</td>
+<td>38418</td>
+<td>76.94</td>
+<td>178 +/- 4</td>
+<td>-0.41 +/- 0.49</td>
+<td>-0.55 +/- 0.23</td>
+<td>83.90</td>
+<td>1.26</td>
+<td>33240</td>
+</tr>
+<tr>
+<td>8</td>
+<td>64363</td>
+<td>0.7900</td>
+<td>0.4600</td>
+<td>2.07</td>
+<td>36968</td>
+<td>62.45</td>
+<td>198 +/- 32</td>
+<td>-0.52 +/- 0.36</td>
+<td>-0.29 +/- 0.19</td>
+<td>79.81</td>
+<td>1.56</td>
+<td>30181</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_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
projects / htsworkflow.git / commitdiff