htsworkflow/pipelines/test/simulate_runfolder.py

   1 """
   2 Create simulated solexa/illumina runfolders for testing
   3 """
   4
   5 import os
   6
   7 def make_firecrest_dir(data_dir, version="1.9.2", start=1, stop=37):
   8     firecrest_dir = os.path.join(data_dir,
   9                                  'C%d-%d_Firecrest%s_12-04-2008_diane' % (start, stop, version)
  10                                  )
  11     os.mkdir(firecrest_dir)
  12     return firecrest_dir
  13
  14 def make_ipar_dir(data_dir):
  15     """
  16     Construct an artificial ipar parameter file and directory
  17     """
  18     params = """<?xml version="1.0"?>
  19 <ImageAnalysis>
  20   <Run Name="IPAR_1.01">
  21     <Software Name="IPAR" Version="2.01.192.0" />
  22     <Cycles First="1" Last="37" Number="37" />
  23     <RunParameters>
  24       <ImagingReads Index="1">
  25         <FirstCycle>1</FirstCycle>
  26         <LastCycle>37</LastCycle>
  27         <RunFolder>081021_HWI-EAS229_0063_30HKUAAXX</RunFolder>
  28       </ImagingReads>
  29       <Reads Index="1">
  30         <FirstCycle>1</FirstCycle>
  31         <LastCycle>37</LastCycle>
  32         <RunFolder>081021_HWI-EAS229_0063_30HKUAAXX</RunFolder>
  33       </Reads>
  34       <Compression>gzip</Compression>
  35       <CompressionSuffix>.p.gz</CompressionSuffix>
  36       <Instrument>HWI-EAS229</Instrument>
  37       <RunFolder>081021_HWI-EAS229_0063_30HKUAAXX</RunFolder>
  38     </RunParameters>
  39     <ImageParameters>
  40       <AutoOffsetFlag>1</AutoOffsetFlag>
  41       <Fwhm>2.7</Fwhm>
  42       <RemappingDistance>1.5</RemappingDistance>
  43       <Threshold>4</Threshold>
  44     </ImageParameters>
  45     <TileSelection>
  46       <Lane Index="1">
  47         <Sample>s</Sample>
  48         <TileRange Max="100" Min="1" />
  49       </Lane>
  50       <Lane Index="2">
  51         <Sample>s</Sample>
  52         <TileRange Max="100" Min="1" />
  53       </Lane>
  54       <Lane Index="3">
  55         <Sample>s</Sample>
  56         <TileRange Max="100" Min="1" />
  57       </Lane>
  58       <Lane Index="4">
  59         <Sample>s</Sample>
  60         <TileRange Max="100" Min="1" />
  61       </Lane>
  62       <Lane Index="5">
  63         <Sample>s</Sample>
  64         <TileRange Max="100" Min="1" />
  65       </Lane>
  66       <Lane Index="6">
  67         <Sample>s</Sample>
  68         <TileRange Max="100" Min="1" />
  69       </Lane>
  70       <Lane Index="7">
  71         <Sample>s</Sample>
  72         <TileRange Max="100" Min="1" />
  73       </Lane>
  74       <Lane Index="8">
  75         <Sample>s</Sample>
  76         <TileRange Max="100" Min="1" />
  77       </Lane>
  78     </TileSelection>
  79   </Run>
  80 </ImageAnalysis>
  81 """
  82     f = open(os.path.join(data_dir, '.params'),'w')
  83     f.write(params)
  84     f.close()
  85     ipar_dir = os.path.join(data_dir, 'IPAR_1.01')
  86     if not os.path.exists(ipar_dir):
  87       os.mkdir(ipar_dir)
  88     return ipar_dir
  89
  90 def make_flowcell_id(runfolder_dir, flowcell_id=None):
  91     if flowcell_id is None:
  92         flowcell_id = '207BTAAXY'
  93
  94     config = """<?xml version="1.0"?>
  95 <FlowcellId>
  96   <Text>%s</Text>
  97 </FlowcellId>""" % (flowcell_id,)
  98     config_dir = os.path.join(runfolder_dir, 'Config')
  99
 100     if not os.path.exists(config_dir):
 101         os.mkdir(config_dir)
 102     pathname = os.path.join(config_dir, 'FlowcellId.xml')
 103     f = open(pathname,'w')
 104     f.write(config)
 105     f.close()
 106
 107 def make_matrix(matrix_dir):
 108     contents = """# Auto-generated frequency response matrix
 109 > A
 110 > C
 111 > G
 112 > T
 113 0.77 0.15 -0.04 -0.04
 114 0.76 1.02 -0.05 -0.06
 115 -0.10 -0.10 1.17 -0.03
 116 -0.13 -0.12 0.80 1.27
 117 """
 118     s_matrix = os.path.join(matrix_dir, 's_matrix.txt')
 119     f = open(s_matrix, 'w')
 120     f.write(contents)
 121     f.close()
 122
 123 def make_phasing_params(bustard_dir):
 124     for lane in range(1,9):
 125         pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
 126         f = open(pathname, 'w')
 127         f.write("""<Parameters>
 128   <Phasing>0.009900</Phasing>
 129   <Prephasing>0.003500</Prephasing>
 130 </Parameters>
 131 """)
 132         f.close()
 133
 134 def make_gerald_config(gerald_dir):
 135     config_xml = """<RunParameters>
 136 <ChipWideRunParameters>
 137   <ANALYSIS>default</ANALYSIS>
 138   <BAD_LANES></BAD_LANES>
 139   <BAD_TILES></BAD_TILES>
 140   <CONTAM_DIR></CONTAM_DIR>
 141   <CONTAM_FILE></CONTAM_FILE>
 142   <ELAND_GENOME>Need_to_specify_ELAND_genome_directory</ELAND_GENOME>
 143   <ELAND_MULTIPLE_INSTANCES>8</ELAND_MULTIPLE_INSTANCES>
 144   <ELAND_REPEAT></ELAND_REPEAT>
 145   <EMAIL_DOMAIN>domain.com</EMAIL_DOMAIN>
 146   <EMAIL_LIST>diane</EMAIL_LIST>
 147   <EMAIL_SERVER>localhost:25</EMAIL_SERVER>
 148   <EXPT_DIR>/home/diane/gec/080416_HWI-EAS229_0024_207BTAAXX/Data/C1-33_Firecrest1.8.28_19-04-2008_diane/Bustard1.8.28_19-04-2008_diane</EXPT_DIR>
 149   <EXPT_DIR_ROOT>/home/diane/gec</EXPT_DIR_ROOT>
 150   <FORCE>1</FORCE>
 151   <GENOME_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald/../../Genomes</GENOME_DIR>
 152   <GENOME_FILE>Need_to_specify_genome_file_name</GENOME_FILE>
 153   <HAMSTER_FLAG>genome</HAMSTER_FLAG>
 154   <OUT_DIR>/home/diane/gec/080416_HWI-EAS229_0024_207BTAAXX/Data/C1-33_Firecrest1.8.28_19-04-2008_diane/Bustard1.8.28_19-04-2008_diane/GERALD_19-04-2008_diane</OUT_DIR>
 155   <POST_RUN_COMMAND></POST_RUN_COMMAND>
 156   <PRB_FILE_SUFFIX>_prb.txt</PRB_FILE_SUFFIX>
 157   <PURE_BASES>12</PURE_BASES>
 158   <QF_PARAMS>'((CHASTITY&gt;=0.6))'</QF_PARAMS>
 159   <QHG_FILE_SUFFIX>_qhg.txt</QHG_FILE_SUFFIX>
 160   <QUALITY_FORMAT>--symbolic</QUALITY_FORMAT>
 161   <READ_LENGTH>32</READ_LENGTH>
 162   <SEQUENCE_FORMAT>--scarf</SEQUENCE_FORMAT>
 163   <SEQ_FILE_SUFFIX>_seq.txt</SEQ_FILE_SUFFIX>
 164   <SIG_FILE_SUFFIX_DEPHASED>_sig2.txt</SIG_FILE_SUFFIX_DEPHASED>
 165   <SIG_FILE_SUFFIX_NOT_DEPHASED>_sig.txt</SIG_FILE_SUFFIX_NOT_DEPHASED>
 166   <SOFTWARE_VERSION>@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp</SOFTWARE_VERSION>
 167   <TILE_REGEX>s_[1-8]_[0-9][0-9][0-9][0-9]</TILE_REGEX>
 168   <TILE_ROOT>s</TILE_ROOT>
 169   <TIME_STAMP>Sat Apr 19 19:08:30 2008</TIME_STAMP>
 170   <TOOLS_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald</TOOLS_DIR>
 171   <USE_BASES>all</USE_BASES>
 172   <WEB_DIR_ROOT>http://host.domain.com/yourshare/</WEB_DIR_ROOT>
 173 </ChipWideRunParameters>
 174 <LaneSpecificRunParameters>
 175   <ANALYSIS>
 176     <s_1>eland</s_1>
 177     <s_2>eland</s_2>
 178     <s_3>eland</s_3>
 179     <s_4>eland</s_4>
 180     <s_5>eland</s_5>
 181     <s_6>eland</s_6>
 182     <s_7>eland</s_7>
 183     <s_8>eland</s_8>
 184   </ANALYSIS>
 185   <ELAND_GENOME>
 186     <s_1>/g/dm3</s_1>
 187     <s_2>/g/equcab1</s_2>
 188     <s_3>/g/equcab1</s_3>
 189     <s_4>/g/canfam2</s_4>
 190     <s_5>/g/hg18</s_5>
 191     <s_6>/g/hg18</s_6>
 192     <s_7>/g/hg18</s_7>
 193     <s_8>/g/hg18</s_8>
 194   </ELAND_GENOME>
 195   <READ_LENGTH>
 196     <s_1>32</s_1>
 197     <s_2>32</s_2>
 198     <s_3>32</s_3>
 199     <s_4>32</s_4>
 200     <s_5>32</s_5>
 201     <s_6>32</s_6>
 202     <s_7>32</s_7>
 203     <s_8>32</s_8>
 204   </READ_LENGTH>
 205   <USE_BASES>
 206     <s_1>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_1>
 207     <s_2>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_2>
 208     <s_3>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_3>
 209     <s_4>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_4>
 210     <s_5>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_5>
 211     <s_6>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_6>
 212     <s_7>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_7>
 213     <s_8>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_8>
 214   </USE_BASES>
 215 </LaneSpecificRunParameters>
 216 </RunParameters>
 217 """
 218     pathname = os.path.join(gerald_dir, 'config.xml')
 219     f = open(pathname,'w')
 220     f.write(config_xml)
 221     f.close()
 222
 223 def make_summary100_htm(gerald_dir):
 224     summary_htm="""<!--RUN_TIME Wed Jul  2 06:47:44 2008 -->
 225 <!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.94 2007/12/04 09:59:07 rshaw Exp $-->
 226 <html>
 227 <body>
 228
 229 <a name="Top"><h2><title>080627_HWI-EAS229_0036_3055HAXX Summary</title></h2></a>
 230 <h1>Summary Information For Experiment 080627_HWI-EAS229_0036_3055HAXX on Machine HWI-EAS229</h1>
 231 <h2><br></br>Chip Summary<br></br></h2>
 232 <table border="1" cellpadding="5">
 233 <tr><td>Machine</td><td>HWI-EAS229</td></tr>
 234 <tr><td>Run Folder</td><td>080627_HWI-EAS229_0036_3055HAXX</td></tr>
 235 <tr><td>Chip ID</td><td>unknown</td></tr>
 236 </table>
 237 <h2><br></br>Chip Results Summary<br></br></h2>
 238 <table border="1" cellpadding="5">
 239 <tr>
 240 <td>Clusters</td>
 241 <td>Clusters (PF)</td>
 242 <td>Yield (kbases)</td>
 243 </tr>
 244 <tr><td>80933224</td>
 245 <td>43577803</td>
 246 <td>1133022</td>
 247 </tr>
 248 </table>
 249 <h2><br></br>Lane Parameter Summary<br></br></h2>
 250 <table border="1" cellpadding="5">
 251 <tr>
 252 <td>Lane</td>
 253 <td>Sample ID</td>
 254 <td>Sample Target</td>
 255 <td>Sample Type</td>
 256 <td>Length</td>
 257 <td>Filter</td>
 258 <td>Num Tiles</td>
 259 <td>Tiles</td>
 260 </tr>
 261 <tr>
 262 <td>1</td>
 263 <td>unknown</td>
 264 <td>mm9</td>
 265 <td>ELAND</td>
 266 <td>26</td>
 267 <td>'((CHASTITY>=0.6))'</td>
 268 <td>100</td>
 269 <td><a href="#Lane1">Lane 1</a></td>
 270 </tr>
 271 <tr>
 272 <td>2</td>
 273 <td>unknown</td>
 274 <td>mm9</td>
 275 <td>ELAND</td>
 276 <td>26</td>
 277 <td>'((CHASTITY>=0.6))'</td>
 278 <td>100</td>
 279 <td><a href="#Lane2">Lane 2</a></td>
 280 </tr>
 281 <tr>
 282 <td>3</td>
 283 <td>unknown</td>
 284 <td>mm9</td>
 285 <td>ELAND</td>
 286 <td>26</td>
 287 <td>'((CHASTITY>=0.6))'</td>
 288 <td>100</td>
 289 <td><a href="#Lane3">Lane 3</a></td>
 290 </tr>
 291 <tr>
 292 <td>4</td>
 293 <td>unknown</td>
 294 <td>elegans170</td>
 295 <td>ELAND</td>
 296 <td>26</td>
 297 <td>'((CHASTITY>=0.6))'</td>
 298 <td>100</td>
 299 <td><a href="#Lane4">Lane 4</a></td>
 300 </tr>
 301 <tr>
 302 <td>5</td>
 303 <td>unknown</td>
 304 <td>elegans170</td>
 305 <td>ELAND</td>
 306 <td>26</td>
 307 <td>'((CHASTITY>=0.6))'</td>
 308 <td>100</td>
 309 <td><a href="#Lane5">Lane 5</a></td>
 310 </tr>
 311 <tr>
 312 <td>6</td>
 313 <td>unknown</td>
 314 <td>elegans170</td>
 315 <td>ELAND</td>
 316 <td>26</td>
 317 <td>'((CHASTITY>=0.6))'</td>
 318 <td>100</td>
 319 <td><a href="#Lane6">Lane 6</a></td>
 320 </tr>
 321 <tr>
 322 <td>7</td>
 323 <td>unknown</td>
 324 <td>elegans170</td>
 325 <td>ELAND</td>
 326 <td>26</td>
 327 <td>'((CHASTITY>=0.6))'</td>
 328 <td>100</td>
 329 <td><a href="#Lane7">Lane 7</a></td>
 330 </tr>
 331 <tr>
 332 <td>8</td>
 333 <td>unknown</td>
 334 <td>elegans170</td>
 335 <td>ELAND</td>
 336 <td>26</td>
 337 <td>'((CHASTITY>=0.6))'</td>
 338 <td>100</td>
 339 <td><a href="#Lane8">Lane 8</a></td>
 340 </tr>
 341 </table>
 342 <h2><br></br>Lane Results Summary<br></br></h2>
 343 <table border="1" cellpadding="5">
 344 <tr>
 345 <td colspan="2">Lane Info</td>
 346 <td colspan="8">Tile Mean +/- SD for Lane</td>
 347 </tr>
 348 <tr>
 349 <td>Lane </td>
 350 <td>Lane Yield (kbases) </td>
 351 <td>Clusters (raw)</td>
 352 <td>Clusters (PF) </td>
 353 <td>1st Cycle Int (PF) </td>
 354 <td>% intensity after 20 cycles (PF) </td>
 355 <td>% PF Clusters </td>
 356 <td>% Align (PF) </td>
 357 <td>Alignment Score (PF) </td>
 358 <td> % Error Rate (PF) </td>
 359 </tr>
 360 <tr>
 361 <td>1</td>
 362 <td>158046</td>
 363 <td>96483 +/- 9074</td>
 364 <td>60787 +/- 4240</td>
 365 <td>329 +/- 35</td>
 366 <td>101.88 +/- 6.03</td>
 367 <td>63.21 +/- 3.29</td>
 368 <td>70.33 +/- 0.24</td>
 369 <td>9054.08 +/- 59.16</td>
 370 <td>0.46 +/- 0.18</td>
 371 </tr>
 372 <tr>
 373 <td>2</td>
 374 <td>156564</td>
 375 <td>133738 +/- 7938</td>
 376 <td>60217 +/- 1926</td>
 377 <td>444 +/- 39</td>
 378 <td>92.62 +/- 7.58</td>
 379 <td>45.20 +/- 3.31</td>
 380 <td>51.98 +/- 0.74</td>
 381 <td>6692.04 +/- 92.49</td>
 382 <td>0.46 +/- 0.09</td>
 383 </tr>
 384 <tr>
 385 <td>3</td>
 386 <td>185818</td>
 387 <td>152142 +/- 10002</td>
 388 <td>71468 +/- 2827</td>
 389 <td>366 +/- 36</td>
 390 <td>91.53 +/- 8.66</td>
 391 <td>47.19 +/- 3.80</td>
 392 <td>82.24 +/- 0.44</td>
 393 <td>10598.68 +/- 64.13</td>
 394 <td>0.41 +/- 0.04</td>
 395 </tr>
 396 <tr>
 397 <td>4</td>
 398 <td>34953</td>
 399 <td>15784 +/- 2162</td>
 400 <td>13443 +/- 1728</td>
 401 <td>328 +/- 40</td>
 402 <td>97.53 +/- 9.87</td>
 403 <td>85.29 +/- 1.91</td>
 404 <td>80.02 +/- 0.53</td>
 405 <td>10368.82 +/- 71.08</td>
 406 <td>0.15 +/- 0.05</td>
 407 </tr>
 408 <tr>
 409 <td>5</td>
 410 <td>167936</td>
 411 <td>119735 +/- 8465</td>
 412 <td>64590 +/- 2529</td>
 413 <td>417 +/- 37</td>
 414 <td>88.69 +/- 14.79</td>
 415 <td>54.10 +/- 2.59</td>
 416 <td>76.95 +/- 0.32</td>
 417 <td>9936.47 +/- 65.75</td>
 418 <td>0.28 +/- 0.02</td>
 419 </tr>
 420 <tr>
 421 <td>6</td>
 422 <td>173463</td>
 423 <td>152177 +/- 8146</td>
 424 <td>66716 +/- 2493</td>
 425 <td>372 +/- 39</td>
 426 <td>87.06 +/- 9.86</td>
 427 <td>43.98 +/- 3.12</td>
 428 <td>78.80 +/- 0.43</td>
 429 <td>10162.28 +/- 49.65</td>
 430 <td>0.38 +/- 0.03</td>
 431 </tr>
 432 <tr>
 433 <td>7</td>
 434 <td>149287</td>
 435 <td>84649 +/- 7325</td>
 436 <td>57418 +/- 3617</td>
 437 <td>295 +/- 28</td>
 438 <td>89.40 +/- 8.23</td>
 439 <td>67.97 +/- 1.82</td>
 440 <td>33.38 +/- 0.25</td>
 441 <td>4247.92 +/- 32.37</td>
 442 <td>1.00 +/- 0.03</td>
 443 </tr>
 444 <tr>
 445 <td>8</td>
 446 <td>106953</td>
 447 <td>54622 +/- 4812</td>
 448 <td>41136 +/- 3309</td>
 449 <td>284 +/- 37</td>
 450 <td>90.21 +/- 9.10</td>
 451 <td>75.39 +/- 2.27</td>
 452 <td>48.33 +/- 0.29</td>
 453 <td>6169.21 +/- 169.50</td>
 454 <td>0.86 +/- 1.22</td>
 455 </tr>
 456 <tr><td colspan="13">Tile mean across chip</td></tr>
 457 <tr>
 458 <td>Av.</td>
 459 <td></td>
 460 <td>101166</td>
 461 <td>54472</td>
 462 <td>354</td>
 463 <td>92.36</td>
 464 <td>60.29</td>
 465 <td>65.25</td>
 466 <td>8403.69</td>
 467 <td>0.50</td>
 468 </tr>
 469 </table>
 470 <h2><br></br>Expanded Lane Summary<br></br></h2>
 471 <table border="1" cellpadding="5">
 472 <tr>
 473
 474 <tr><td colspan="2">Lane Info</td>
 475 <td colspan="2">Phasing Info</td>
 476 <td colspan="2">Raw Data (tile mean)</td>
 477 <td colspan="7">Filtered Data (tile mean)</td></tr>
 478 <td>Lane </td>
 479 <td>Clusters (tile mean) (raw)</td>
 480 <td>% Phasing </td>
 481 <td>% Prephasing </td>
 482 <td>% Error Rate (raw) </td>
 483 <td> Equiv Perfect Clusters (raw) </td>
 484 <td>% retained </td>
 485 <td>Cycle 2-4 Av Int (PF) </td>
 486 <td>Cycle 2-10 Av % Loss (PF) </td>
 487 <td>Cycle 10-20 Av % Loss (PF) </td>
 488 <td>% Align (PF) </td>
 489 <td>% Error Rate (PF) </td>
 490 <td> Equiv Perfect Clusters (PF) </td>
 491 </tr>
 492 <tr>
 493 <td>1</td>
 494 <td>96483</td>
 495 <td>0.7700</td>
 496 <td>0.3100</td>
 497 <td>1.00</td>
 498 <td>49676</td>
 499 <td>63.21</td>
 500 <td>317 +/- 32</td>
 501 <td>0.13 +/- 0.44</td>
 502 <td>-1.14 +/- 0.34</td>
 503 <td>70.33</td>
 504 <td>0.46</td>
 505 <td>41758</td>
 506 </tr>
 507 <tr>
 508 <td>2</td>
 509 <td>133738</td>
 510 <td>0.7700</td>
 511 <td>0.3100</td>
 512 <td>1.22</td>
 513 <td>40467</td>
 514 <td>45.20</td>
 515 <td>415 +/- 33</td>
 516 <td>0.29 +/- 0.40</td>
 517 <td>-0.79 +/- 0.35</td>
 518 <td>51.98</td>
 519 <td>0.46</td>
 520 <td>30615</td>
 521 </tr>
 522 <tr>
 523 <td>3</td>
 524 <td>152142</td>
 525 <td>0.7700</td>
 526 <td>0.3100</td>
 527 <td>1.30</td>
 528 <td>78588</td>
 529 <td>47.19</td>
 530 <td>344 +/- 26</td>
 531 <td>0.68 +/- 0.51</td>
 532 <td>-0.77 +/- 0.42</td>
 533 <td>82.24</td>
 534 <td>0.41</td>
 535 <td>57552</td>
 536 </tr>
 537 <tr>
 538 <td>4</td>
 539 <td>15784</td>
 540 <td>0.7700</td>
 541 <td>0.3100</td>
 542 <td>0.29</td>
 543 <td>11095</td>
 544 <td>85.29</td>
 545 <td>306 +/- 34</td>
 546 <td>0.20 +/- 0.69</td>
 547 <td>-1.28 +/- 0.66</td>
 548 <td>80.02</td>
 549 <td>0.15</td>
 550 <td>10671</td>
 551 </tr>
 552 <tr>
 553 <td>5</td>
 554 <td>119735</td>
 555 <td>0.7700</td>
 556 <td>0.3100</td>
 557 <td>0.85</td>
 558 <td>60335</td>
 559 <td>54.10</td>
 560 <td>380 +/- 32</td>
 561 <td>0.34 +/- 0.49</td>
 562 <td>-1.55 +/- 4.69</td>
 563 <td>76.95</td>
 564 <td>0.28</td>
 565 <td>49015</td>
 566 </tr>
 567 <tr>
 568 <td>6</td>
 569 <td>152177</td>
 570 <td>0.7700</td>
 571 <td>0.3100</td>
 572 <td>1.21</td>
 573 <td>70905</td>
 574 <td>43.98</td>
 575 <td>333 +/- 27</td>
 576 <td>0.57 +/- 0.50</td>
 577 <td>-0.91 +/- 0.39</td>
 578 <td>78.80</td>
 579 <td>0.38</td>
 580 <td>51663</td>
 581 </tr>
 582 <tr>
 583 <td>7</td>
 584 <td>84649</td>
 585 <td>0.7700</td>
 586 <td>0.3100</td>
 587 <td>1.38</td>
 588 <td>21069</td>
 589 <td>67.97</td>
 590 <td>272 +/- 20</td>
 591 <td>1.15 +/- 0.52</td>
 592 <td>-0.84 +/- 0.58</td>
 593 <td>33.38</td>
 594 <td>1.00</td>
 595 <td>18265</td>
 596 </tr>
 597 <tr>
 598 <td>8</td>
 599 <td>54622</td>
 600 <td>0.7700</td>
 601 <td>0.3100</td>
 602 <td>1.17</td>
 603 <td>21335</td>
 604 <td>75.39</td>
 605 <td>262 +/- 31</td>
 606 <td>1.10 +/- 0.59</td>
 607 <td>-1.01 +/- 0.47</td>
 608 <td>48.33</td>
 609 <td>0.86</td>
 610 <td>19104</td>
 611 </tr>
 612 </table>
 613 <b><br></br>IVC Plots</b>
 614 <p> <a href='IVC.htm' target="_blank"> IVC.htm
 615  </a></p>
 616 <b><br></br>All Intensity Plots</b>
 617 <p> <a href='All.htm' target="_blank"> All.htm
 618  </a></p>
 619 <b><br></br>Error graphs: </b>
 620 <p> <a href='Error.htm' target="_blank"> Error.htm
 621  </a></p>
 622 <td><a href="#Top">Back to top</a></td>
 623 <a name="Lane1"><h2><br></br>Lane 1<br></br></h2></a>
 624 <table border="1" cellpadding="5">
 625 <tr>
 626 <td>Lane </td>
 627 <td>Tile </td>
 628 <td>Clusters (raw)</td>
 629 <td>Av 1st Cycle Int (PF) </td>
 630 <td>Av % intensity after 20 cycles (PF) </td>
 631 <td>% PF Clusters </td>
 632 <td>% Align (PF) </td>
 633 <td>Av Alignment Score (PF) </td>
 634 <td>% Error Rate (PF) </td>
 635 </tr>
 636 <tr>
 637 <td>1</td>
 638 <td>0001</td>
 639 <td>114972</td>
 640 <td>326.48</td>
 641 <td>94.39</td>
 642 <td>57.44</td>
 643 <td>70.2</td>
 644 <td>9038.6</td>
 645 <td>0.44</td>
 646 </tr>
 647 </table>
 648 <td><a href="#Top">Back to top</a></td>
 649 <a name="Lane2"><h2><br></br>Lane 2<br></br></h2></a>
 650 <table border="1" cellpadding="5">
 651 <tr>
 652 <td>Lane </td>
 653 <td>Tile </td>
 654 <td>Clusters (raw)</td>
 655 <td>Av 1st Cycle Int (PF) </td>
 656 <td>Av % intensity after 20 cycles (PF) </td>
 657 <td>% PF Clusters </td>
 658 <td>% Align (PF) </td>
 659 <td>Av Alignment Score (PF) </td>
 660 <td>% Error Rate (PF) </td>
 661 </tr>
 662 <tr>
 663 <td>2</td>
 664 <td>0001</td>
 665 <td>147793</td>
 666 <td>448.12</td>
 667 <td>83.68</td>
 668 <td>38.57</td>
 669 <td>53.7</td>
 670 <td>6905.4</td>
 671 <td>0.54</td>
 672 </tr>
 673 </table>
 674 <td><a href="#Top">Back to top</a></td>
 675 <a name="Lane3"><h2><br></br>Lane 3<br></br></h2></a>
 676 <table border="1" cellpadding="5">
 677 <tr>
 678 <td>Lane </td>
 679 <td>Tile </td>
 680 <td>Clusters (raw)</td>
 681 <td>Av 1st Cycle Int (PF) </td>
 682 <td>Av % intensity after 20 cycles (PF) </td>
 683 <td>% PF Clusters </td>
 684 <td>% Align (PF) </td>
 685 <td>Av Alignment Score (PF) </td>
 686 <td>% Error Rate (PF) </td>
 687 </tr>
 688 <tr>
 689 <td>3</td>
 690 <td>0001</td>
 691 <td>167904</td>
 692 <td>374.05</td>
 693 <td>86.91</td>
 694 <td>40.36</td>
 695 <td>81.3</td>
 696 <td>10465.0</td>
 697 <td>0.47</td>
 698 </tr>
 699 </table>
 700 <td><a href="#Top">Back to top</a></td>
 701 <a name="Lane4"><h2><br></br>Lane 4<br></br></h2></a>
 702 <table border="1" cellpadding="5">
 703 <tr>
 704 <td>Lane </td>
 705 <td>Tile </td>
 706 <td>Clusters (raw)</td>
 707 <td>Av 1st Cycle Int (PF) </td>
 708 <td>Av % intensity after 20 cycles (PF) </td>
 709 <td>% PF Clusters </td>
 710 <td>% Align (PF) </td>
 711 <td>Av Alignment Score (PF) </td>
 712 <td>% Error Rate (PF) </td>
 713 </tr>
 714 <tr>
 715 <td>4</td>
 716 <td>0001</td>
 717 <td>20308</td>
 718 <td>276.85</td>
 719 <td>92.87</td>
 720 <td>84.26</td>
 721 <td>80.4</td>
 722 <td>10413.8</td>
 723 <td>0.16</td>
 724 </tr>
 725 </table>
 726 <td><a href="#Top">Back to top</a></td>
 727 <a name="Lane5"><h2><br></br>Lane 5<br></br></h2></a>
 728 <table border="1" cellpadding="5">
 729 <tr>
 730 <td>Lane </td>
 731 <td>Tile </td>
 732 <td>Clusters (raw)</td>
 733 <td>Av 1st Cycle Int (PF) </td>
 734 <td>Av % intensity after 20 cycles (PF) </td>
 735 <td>% PF Clusters </td>
 736 <td>% Align (PF) </td>
 737 <td>Av Alignment Score (PF) </td>
 738 <td>% Error Rate (PF) </td>
 739 </tr>
 740 </table>
 741 <td><a href="#Top">Back to top</a></td>
 742 <a name="Lane6"><h2><br></br>Lane 6<br></br></h2></a>
 743 <table border="1" cellpadding="5">
 744 <tr>
 745 <td>Lane </td>
 746 <td>Tile </td>
 747 <td>Clusters (raw)</td>
 748 <td>Av 1st Cycle Int (PF) </td>
 749 <td>Av % intensity after 20 cycles (PF) </td>
 750 <td>% PF Clusters </td>
 751 <td>% Align (PF) </td>
 752 <td>Av Alignment Score (PF) </td>
 753 <td>% Error Rate (PF) </td>
 754 </tr>
 755 <tr>
 756 <td>6</td>
 757 <td>0001</td>
 758 <td>166844</td>
 759 <td>348.12</td>
 760 <td>77.59</td>
 761 <td>38.13</td>
 762 <td>79.7</td>
 763 <td>10264.4</td>
 764 <td>0.44</td>
 765 </tr>
 766 </table>
 767 <td><a href="#Top">Back to top</a></td>
 768 <a name="Lane7"><h2><br></br>Lane 7<br></br></h2></a>
 769 <table border="1" cellpadding="5">
 770 <tr>
 771 <td>Lane </td>
 772 <td>Tile </td>
 773 <td>Clusters (raw)</td>
 774 <td>Av 1st Cycle Int (PF) </td>
 775 <td>Av % intensity after 20 cycles (PF) </td>
 776 <td>% PF Clusters </td>
 777 <td>% Align (PF) </td>
 778 <td>Av Alignment Score (PF) </td>
 779 <td>% Error Rate (PF) </td>
 780 </tr>
 781 <tr>
 782 <td>7</td>
 783 <td>0001</td>
 784 <td>98913</td>
 785 <td>269.90</td>
 786 <td>86.66</td>
 787 <td>64.55</td>
 788 <td>33.2</td>
 789 <td>4217.5</td>
 790 <td>1.02</td>
 791 </tr>
 792 </table>
 793 <td><a href="#Top">Back to top</a></td>
 794 <a name="Lane8"><h2><br></br>Lane 8<br></br></h2></a>
 795 <table border="1" cellpadding="5">
 796 <tr>
 797 <td>Lane </td>
 798 <td>Tile </td>
 799 <td>Clusters (raw)</td>
 800 <td>Av 1st Cycle Int (PF) </td>
 801 <td>Av % intensity after 20 cycles (PF) </td>
 802 <td>% PF Clusters </td>
 803 <td>% Align (PF) </td>
 804 <td>Av Alignment Score (PF) </td>
 805 <td>% Error Rate (PF) </td>
 806 </tr>
 807 <tr>
 808 <td>8</td>
 809 <td>0001</td>
 810 <td>64972</td>
 811 <td>243.60</td>
 812 <td>89.40</td>
 813 <td>73.17</td>
 814 <td>48.3</td>
 815 <td>6182.8</td>
 816 <td>0.71</td>
 817 </tr>
 818 </table>
 819 <td><a href="#Top">Back to top</a></td>
 820 </body>
 821 </html>
 822 """
 823     pathname = os.path.join(gerald_dir, 'Summary.htm')
 824     f = open(pathname, 'w')
 825     f.write(summary_htm)
 826     f.close()
 827
 828 def make_summary_htm_110(gerald_dir):
 829     summary_htm = """<!--RUN_TIME Tue Oct 28 09:45:50 2008 -->
 830 <!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.10 2008/07/23 15:18:30 mzerara Exp $-->
 831 <html>
 832 <body>
 833
 834 <a name="Top"><h2><title>081017_HWI-EAS229_0062_30J55AAXX Summary</title></h2></a>
 835 <h1>Summary Information For Experiment 081017_HWI-EAS229_0062_30J55AAXX on Machine HWI-EAS229</h1>
 836 <h2><br></br>Chip Summary<br></br></h2>
 837 <table border="1" cellpadding="5">
 838 <tr><td>Machine</td><td>HWI-EAS229</td></tr>
 839 <tr><td>Run Folder</td><td>081017_HWI-EAS229_0062_30J55AAXX</td></tr>
 840 <tr><td>Chip ID</td><td>unknown</td></tr>
 841 </table>
 842 <h2><br></br>Chip Results Summary<br></br></h2>
 843 <table border="1" cellpadding="5">
 844 <tr>
 845 <td>Clusters</td>
 846 <td>Clusters (PF)</td>
 847 <td>Yield (kbases)</td>
 848 </tr>
 849 <tr><td>162491175</td>
 850 <td>99622159</td>
 851 <td>3686019</td>
 852 </tr>
 853 </table>
 854 <h2><br></br>Lane Parameter Summary<br></br></h2>
 855 <table border="1" cellpadding="5">
 856 <tr>
 857 <td>Lane</td>
 858 <td>Sample ID</td>
 859 <td>Sample Target</td>
 860 <td>Sample Type</td>
 861 <td>Length</td>
 862 <td>Filter</td>
 863 <td>Chast. Thresh.</td>
 864 <td>Num Tiles</td>
 865 <td>Tiles</td>
 866 </tr>
 867 <tr>
 868 <td>1</td>
 869 <td>unknown</td>
 870 <td>mm9</td>
 871 <td>ELAND</td>
 872 <td>37</td>
 873 <td>'((FAILED_CHASTITY<=1))'</td>
 874 <td>0.6</td>
 875 <td>100</td>
 876 <td><a href="#Lane1">Lane 1</a></td>
 877 </tr>
 878 <tr>
 879 <td>2</td>
 880 <td>unknown</td>
 881 <td>mm9</td>
 882 <td>ELAND</td>
 883 <td>37</td>
 884 <td>'((FAILED_CHASTITY<=1))'</td>
 885 <td>0.6</td>
 886 <td>100</td>
 887 <td><a href="#Lane2">Lane 2</a></td>
 888 </tr>
 889 <tr>
 890 <td>3</td>
 891 <td>unknown</td>
 892 <td>mm9</td>
 893 <td>ELAND</td>
 894 <td>37</td>
 895 <td>'((FAILED_CHASTITY<=1))'</td>
 896 <td>0.6</td>
 897 <td>100</td>
 898 <td><a href="#Lane3">Lane 3</a></td>
 899 </tr>
 900 <tr>
 901 <td>4</td>
 902 <td>unknown</td>
 903 <td>hg18</td>
 904 <td>ELAND</td>
 905 <td>37</td>
 906 <td>'((FAILED_CHASTITY<=1))'</td>
 907 <td>0.6</td>
 908 <td>100</td>
 909 <td><a href="#Lane4">Lane 4</a></td>
 910 </tr>
 911 <tr>
 912 <td>5</td>
 913 <td>unknown</td>
 914 <td>hg18</td>
 915 <td>ELAND</td>
 916 <td>37</td>
 917 <td>'((FAILED_CHASTITY<=1))'</td>
 918 <td>0.6</td>
 919 <td>100</td>
 920 <td><a href="#Lane5">Lane 5</a></td>
 921 </tr>
 922 <tr>
 923 <td>6</td>
 924 <td>unknown</td>
 925 <td>mm9</td>
 926 <td>ELAND</td>
 927 <td>37</td>
 928 <td>'((FAILED_CHASTITY<=1))'</td>
 929 <td>0.6</td>
 930 <td>100</td>
 931 <td><a href="#Lane6">Lane 6</a></td>
 932 </tr>
 933 <tr>
 934 <td>7</td>
 935 <td>unknown</td>
 936 <td>mm9</td>
 937 <td>ELAND</td>
 938 <td>37</td>
 939 <td>'((FAILED_CHASTITY<=1))'</td>
 940 <td>0.6</td>
 941 <td>100</td>
 942 <td><a href="#Lane7">Lane 7</a></td>
 943 </tr>
 944 <tr>
 945 <td>8</td>
 946 <td>unknown</td>
 947 <td>mm9</td>
 948 <td>ELAND</td>
 949 <td>37</td>
 950 <td>'((FAILED_CHASTITY<=1))'</td>
 951 <td>0.6</td>
 952 <td>100</td>
 953 <td><a href="#Lane8">Lane 8</a></td>
 954 </tr>
 955 </table>
 956 <h2><br></br>Lane Results Summary<br></br></h2>
 957 <table border="1" cellpadding="5">
 958 <tr>
 959 <td colspan="2">Lane Info</td>
 960 <td colspan="8">Tile Mean +/- SD for Lane</td>
 961 </tr>
 962 <tr>
 963 <td>Lane </td>
 964 <td>Lane Yield (kbases) </td>
 965 <td>Clusters (raw)</td>
 966 <td>Clusters (PF) </td>
 967 <td>1st Cycle Int (PF) </td>
 968 <td>% intensity after 20 cycles (PF) </td>
 969 <td>% PF Clusters </td>
 970 <td>% Align (PF) </td>
 971 <td>Alignment Score (PF) </td>
 972 <td> % Error Rate (PF) </td>
 973 </tr>
 974 <tr>
 975 <td>1</td>
 976 <td>435340</td>
 977 <td>190220 +/- 15118</td>
 978 <td>117659 +/- 8144</td>
 979 <td>273 +/- 16</td>
 980 <td>80.02 +/- 2.52</td>
 981 <td>62.15 +/- 5.54</td>
 982 <td>77.18 +/- 0.22</td>
 983 <td>13447.28 +/- 43.35</td>
 984 <td>2.78 +/- 0.13</td>
 985 </tr>
 986 <tr>
 987 <td>2</td>
 988 <td>462364</td>
 989 <td>190560 +/- 14399</td>
 990 <td>124963 +/- 5687</td>
 991 <td>271 +/- 16</td>
 992 <td>75.73 +/- 2.46</td>
 993 <td>65.83 +/- 4.12</td>
 994 <td>70.06 +/- 0.39</td>
 995 <td>12082.95 +/- 64.81</td>
 996 <td>3.22 +/- 0.09</td>
 997 </tr>
 998 <tr>
 999 <td>3</td>
1000 <td>468929</td>
1001 <td>187597 +/- 12369</td>
1002 <td>126737 +/- 5549</td>
1003 <td>274 +/- 16</td>
1004 <td>72.61 +/- 2.67</td>
1005 <td>67.69 +/- 2.72</td>
1006 <td>74.03 +/- 0.22</td>
1007 <td>12470.18 +/- 50.02</td>
1008 <td>4.27 +/- 0.08</td>
1009 </tr>
1010 <tr>
1011 <td>4</td>
1012 <td>491642</td>
1013 <td>204142 +/- 16877</td>
1014 <td>132876 +/- 4023</td>
1015 <td>253 +/- 16</td>
1016 <td>80.43 +/- 3.10</td>
1017 <td>65.39 +/- 3.84</td>
1018 <td>72.95 +/- 0.15</td>
1019 <td>13273.80 +/- 39.75</td>
1020 <td>0.78 +/- 0.10</td>
1021 </tr>
1022 <tr>
1023 <td>5</td>
1024 <td>433033</td>
1025 <td>247308 +/- 11600</td>
1026 <td>117036 +/- 4489</td>
1027 <td>273 +/- 11</td>
1028 <td>68.60 +/- 2.40</td>
1029 <td>47.48 +/- 3.63</td>
1030 <td>66.91 +/- 0.54</td>
1031 <td>11700.08 +/- 66.33</td>
1032 <td>2.62 +/- 0.13</td>
1033 </tr>
1034 <tr>
1035 <td>6</td>
1036 <td>483012</td>
1037 <td>204298 +/- 15640</td>
1038 <td>130543 +/- 6972</td>
1039 <td>254 +/- 11</td>
1040 <td>81.35 +/- 1.96</td>
1041 <td>64.14 +/- 4.40</td>
1042 <td>77.28 +/- 0.11</td>
1043 <td>14084.01 +/- 23.09</td>
1044 <td>0.71 +/- 0.03</td>
1045 </tr>
1046 <tr>
1047 <td>7</td>
1048 <td>474325</td>
1049 <td>202707 +/- 15404</td>
1050 <td>128196 +/- 9745</td>
1051 <td>255 +/- 13</td>
1052 <td>79.95 +/- 2.08</td>
1053 <td>63.48 +/- 5.63</td>
1054 <td>75.78 +/- 0.18</td>
1055 <td>13758.74 +/- 60.86</td>
1056 <td>0.88 +/- 0.12</td>
1057 </tr>
1058 <tr>
1059 <td>8</td>
1060 <td>437372</td>
1061 <td>198075 +/- 14702</td>
1062 <td>118208 +/- 14798</td>
1063 <td>259 +/- 14</td>
1064 <td>81.80 +/- 2.53</td>
1065 <td>59.85 +/- 7.67</td>
1066 <td>74.55 +/- 0.36</td>
1067 <td>13586.07 +/- 103.97</td>
1068 <td>0.71 +/- 0.15</td>
1069 </tr>
1070 <tr><td colspan="13">Tile mean across chip</td></tr>
1071 <tr>
1072 <td>Av.</td>
1073 <td></td>
1074 <td>203113</td>
1075 <td>124527</td>
1076 <td>264</td>
1077 <td>77.56</td>
1078 <td>62.00</td>
1079 <td>73.59</td>
1080 <td>13050.39</td>
1081 <td>2.00</td>
1082 </tr>
1083 </table>
1084 <h2><br></br>Expanded Lane Summary<br></br></h2>
1085 <table border="1" cellpadding="5">
1086 <tr>
1087
1088 <tr><td colspan="2">Lane Info</td>
1089 <td colspan="2">Phasing Info</td>
1090 <td colspan="2">Raw Data (tile mean)</td>
1091 <td colspan="7">Filtered Data (tile mean)</td></tr>
1092 <td>Lane </td>
1093 <td>Clusters (tile mean) (raw)</td>
1094 <td>% Phasing </td>
1095 <td>% Prephasing </td>
1096 <td>% Error Rate (raw) </td>
1097 <td> Equiv Perfect Clusters (raw) </td>
1098 <td>% retained </td>
1099 <td>Cycle 2-4 Av Int (PF) </td>
1100 <td>Cycle 2-10 Av % Loss (PF) </td>
1101 <td>Cycle 10-20 Av % Loss (PF) </td>
1102 <td>% Align (PF) </td>
1103 <td>% Error Rate (PF) </td>
1104 <td> Equiv Perfect Clusters (PF) </td>
1105 </tr>
1106 <tr>
1107 <td>1</td>
1108 <td>190220</td>
1109 <td>0.6800</td>
1110 <td>0.2800</td>
1111 <td>3.17</td>
1112 <td>107262</td>
1113 <td>62.15</td>
1114 <td>241 +/- 13</td>
1115 <td>0.56 +/- 0.22</td>
1116 <td>0.29 +/- 0.14</td>
1117 <td>77.18</td>
1118 <td>2.78</td>
1119 <td>86184</td>
1120 </tr>
1121 <tr>
1122 <td>2</td>
1123 <td>190560</td>
1124 <td>0.6800</td>
1125 <td>0.2800</td>
1126 <td>3.53</td>
1127 <td>98678</td>
1128 <td>65.83</td>
1129 <td>238 +/- 14</td>
1130 <td>0.78 +/- 0.15</td>
1131 <td>0.53 +/- 0.15</td>
1132 <td>70.06</td>
1133 <td>3.22</td>
1134 <td>83090</td>
1135 </tr>
1136 <tr>
1137 <td>3</td>
1138 <td>187597</td>
1139 <td>0.6800</td>
1140 <td>0.2800</td>
1141 <td>4.44</td>
1142 <td>104008</td>
1143 <td>67.69</td>
1144 <td>233 +/- 14</td>
1145 <td>0.56 +/- 0.17</td>
1146 <td>0.59 +/- 0.26</td>
1147 <td>74.03</td>
1148 <td>4.27</td>
1149 <td>89278</td>
1150 </tr>
1151 <tr>
1152 <td>4</td>
1153 <td>204142</td>
1154 <td>0.6800</td>
1155 <td>0.2800</td>
1156 <td>1.38</td>
1157 <td>115765</td>
1158 <td>65.39</td>
1159 <td>239 +/- 14</td>
1160 <td>1.28 +/- 0.21</td>
1161 <td>0.77 +/- 0.21</td>
1162 <td>72.95</td>
1163 <td>0.78</td>
1164 <td>93475</td>
1165 </tr>
1166 <tr>
1167 <td>5</td>
1168 <td>247308</td>
1169 <td>0.6800</td>
1170 <td>0.2800</td>
1171 <td>3.40</td>
1172 <td>103006</td>
1173 <td>47.48</td>
1174 <td>242 +/- 10</td>
1175 <td>1.61 +/- 0.39</td>
1176 <td>1.21 +/- 0.21</td>
1177 <td>66.91</td>
1178 <td>2.62</td>
1179 <td>73768</td>
1180 </tr>
1181 <tr>
1182 <td>6</td>
1183 <td>204298</td>
1184 <td>0.6800</td>
1185 <td>0.2800</td>
1186 <td>1.33</td>
1187 <td>122233</td>
1188 <td>64.14</td>
1189 <td>242 +/- 12</td>
1190 <td>1.30 +/- 0.11</td>
1191 <td>0.73 +/- 0.22</td>
1192 <td>77.28</td>
1193 <td>0.71</td>
1194 <td>97646</td>
1195 </tr>
1196 <tr>
1197 <td>7</td>
1198 <td>202707</td>
1199 <td>0.6800</td>
1200 <td>0.2800</td>
1201 <td>1.51</td>
1202 <td>117513</td>
1203 <td>63.48</td>
1204 <td>238 +/- 13</td>
1205 <td>1.27 +/- 0.38</td>
1206 <td>0.66 +/- 0.22</td>
1207 <td>75.78</td>
1208 <td>0.88</td>
1209 <td>93659</td>
1210 </tr>
1211 <tr>
1212 <td>8</td>
1213 <td>198075</td>
1214 <td>0.6800</td>
1215 <td>0.2800</td>
1216 <td>1.41</td>
1217 <td>111115</td>
1218 <td>59.85</td>
1219 <td>244 +/- 12</td>
1220 <td>1.19 +/- 0.16</td>
1221 <td>0.65 +/- 0.29</td>
1222 <td>74.55</td>
1223 <td>0.71</td>
1224 <td>85327</td>
1225 </tr>
1226 </table>
1227 </body>
1228 </html>"""
1229     pathname = os.path.join(gerald_dir, 'Summary.htm')
1230     f = open(pathname, 'w')
1231     f.write(summary_htm)
1232     f.close()
1233
1234 def make_summary_paired_htm(gerald_dir):
1235     summary_htm = """<!--RUN_TIME Thu Nov 13 15:11:29 2008 -->
1236 <!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.94 2007/12/04 09:59:07 rshaw Exp $-->
1237 <html>
1238 <body>
1239
1240 <a name="Top"><h2><title>080920_HWI-EAS229_0057_30GBJAAXX Summary</title></h2></a>
1241 <h1>Summary Information For Experiment 080920_HWI-EAS229_0057_30GBJAAXX on Machine unknown</h1>
1242 <h2><br></br>Chip Summary<br></br></h2>
1243 <table border="1" cellpadding="5">
1244 <tr><td>Machine</td><td>UNKNOWN</td></tr>
1245 <tr><td>Run Folder</td><td>080920_HWI-EAS229_0057_30GBJAAXX</td></tr>
1246 <tr><td>Chip ID</td><td>unknown</td></tr>
1247 </table>
1248 <h2><br></br>Chip Results Summary<br></br></h2>
1249 <table border="1" cellpadding="5">
1250 <tr>
1251 <td>Clusters</td>
1252 <td>Clusters (PF)</td>
1253 <td>Yield (kbases)</td>
1254 </tr>
1255 <tr><td>126151880</td>
1256 <td>95923456</td>
1257 <td>3549167</td>
1258 </tr>
1259 </table>
1260 <h2><br></br>Lane Parameter Summary<br></br></h2>
1261 <table border="1" cellpadding="5">
1262 <tr>
1263 <td>Lane</td>
1264 <td>Sample ID</td>
1265 <td>Sample Target</td>
1266 <td>Sample Type</td>
1267 <td>Length</td>
1268 <td>Filter</td>
1269 <td>Num Tiles</td>
1270 <td>Tiles</td>
1271 </tr>
1272 <tr>
1273 <td>1</td>
1274 <td>unknown</td>
1275 <td>mm9</td>
1276 <td>ELAND_PAIR</td>
1277 <td>37, 37</td>
1278 <td>'((CHASTITY>=0.6))'</td>
1279 <td>100</td>
1280 <td><a href="#Lane1">Lane 1</a></td>
1281 </tr>
1282 <tr>
1283 <td>2</td>
1284 <td>unknown</td>
1285 <td>hg18</td>
1286 <td>ELAND_PAIR</td>
1287 <td>37, 37</td>
1288 <td>'((CHASTITY>=0.6))'</td>
1289 <td>100</td>
1290 <td><a href="#Lane2">Lane 2</a></td>
1291 </tr>
1292 <tr>
1293 <td>3</td>
1294 <td>unknown</td>
1295 <td>mm9</td>
1296 <td>ELAND_PAIR</td>
1297 <td>37, 37</td>
1298 <td>'((CHASTITY>=0.6))'</td>
1299 <td>100</td>
1300 <td><a href="#Lane3">Lane 3</a></td>
1301 </tr>
1302 <tr>
1303 <td>4</td>
1304 <td>unknown</td>
1305 <td>mm9</td>
1306 <td>ELAND_PAIR</td>
1307 <td>37, 37</td>
1308 <td>'((CHASTITY>=0.6))'</td>
1309 <td>100</td>
1310 <td><a href="#Lane4">Lane 4</a></td>
1311 </tr>
1312 <tr>
1313 <td>5</td>
1314 <td>unknown</td>
1315 <td>mm9</td>
1316 <td>ELAND_PAIR</td>
1317 <td>37, 37</td>
1318 <td>'((CHASTITY>=0.6))'</td>
1319 <td>100</td>
1320 <td><a href="#Lane5">Lane 5</a></td>
1321 </tr>
1322 <tr>
1323 <td>6</td>
1324 <td>unknown</td>
1325 <td>hg18</td>
1326 <td>ELAND_PAIR</td>
1327 <td>37, 37</td>
1328 <td>'((CHASTITY>=0.6))'</td>
1329 <td>100</td>
1330 <td><a href="#Lane6">Lane 6</a></td>
1331 </tr>
1332 <tr>
1333 <td>7</td>
1334 <td>unknown</td>
1335 <td>mm9</td>
1336 <td>ELAND_PAIR</td>
1337 <td>37, 37</td>
1338 <td>'((CHASTITY>=0.6))'</td>
1339 <td>100</td>
1340 <td><a href="#Lane7">Lane 7</a></td>
1341 </tr>
1342 <tr>
1343 <td>8</td>
1344 <td>unknown</td>
1345 <td>mm9</td>
1346 <td>ELAND_PAIR</td>
1347 <td>37, 37</td>
1348 <td>'((CHASTITY>=0.6))'</td>
1349 <td>100</td>
1350 <td><a href="#Lane8">Lane 8</a></td>
1351 </tr>
1352 </table>
1353 <h2><br></br>Lane Results Summary : Read 1<br></br></h2>
1354 <table border="1" cellpadding="5">
1355 <tr>
1356 <td colspan="2">Lane Info</td>
1357 <td colspan="8">Tile Mean +/- SD for Lane</td>
1358 </tr>
1359 <tr>
1360 <td>Lane </td>
1361 <td>Lane Yield (kbases) </td>
1362 <td>Clusters (raw)</td>
1363 <td>Clusters (PF) </td>
1364 <td>1st Cycle Int (PF) </td>
1365 <td>% intensity after 20 cycles (PF) </td>
1366 <td>% PF Clusters </td>
1367 <td>% Align (PF) </td>
1368 <td>Alignment Score (PF) </td>
1369 <td> % Error Rate (PF) </td>
1370 </tr>
1371 <tr>
1372 <td>1</td>
1373 <td>277083</td>
1374 <td>103646 +/- 4515</td>
1375 <td>74887 +/- 6080</td>
1376 <td>290 +/- 17</td>
1377 <td>99.34 +/- 3.52</td>
1378 <td>72.22 +/- 4.63</td>
1379 <td>89.19 +/- 0.59</td>
1380 <td>14.16 +/- 0.63</td>
1381 <td>0.94 +/- 0.17</td>
1382 </tr>
1383 <tr>
1384 <td>2</td>
1385 <td>289563</td>
1386 <td>106678 +/- 4652</td>
1387 <td>78260 +/- 2539</td>
1388 <td>294 +/- 16</td>
1389 <td>98.23 +/- 2.66</td>
1390 <td>73.43 +/- 2.52</td>
1391 <td>87.05 +/- 0.64</td>
1392 <td>16.81 +/- 0.55</td>
1393 <td>0.92 +/- 0.17</td>
1394 </tr>
1395 <tr>
1396 <td>3</td>
1397 <td>259242</td>
1398 <td>84583 +/- 5963</td>
1399 <td>70065 +/- 4194</td>
1400 <td>284 +/- 18</td>
1401 <td>99.82 +/- 3.05</td>
1402 <td>82.90 +/- 1.32</td>
1403 <td>89.49 +/- 0.20</td>
1404 <td>18.13 +/- 0.66</td>
1405 <td>0.81 +/- 0.13</td>
1406 </tr>
1407 <tr>
1408 <td>4</td>
1409 <td>210549</td>
1410 <td>68813 +/- 4782</td>
1411 <td>56905 +/- 4145</td>
1412 <td>300 +/- 29</td>
1413 <td>102.00 +/- 14.74</td>
1414 <td>82.91 +/- 5.89</td>
1415 <td>56.93 +/- 0.82</td>
1416 <td>25.85 +/- 2.30</td>
1417 <td>0.95 +/- 0.30</td>
1418 </tr>
1419 <tr>
1420 <td>5</td>
1421 <td>295555</td>
1422 <td>104854 +/- 4664</td>
1423 <td>79879 +/- 6270</td>
1424 <td>281 +/- 19</td>
1425 <td>98.26 +/- 5.85</td>
1426 <td>76.34 +/- 6.67</td>
1427 <td>57.71 +/- 0.30</td>
1428 <td>26.16 +/- 1.68</td>
1429 <td>0.97 +/- 0.19</td>
1430 </tr>
1431 <tr>
1432 <td>6</td>
1433 <td>140401</td>
1434 <td>43555 +/- 1632</td>
1435 <td>37946 +/- 2140</td>
1436 <td>233 +/- 16</td>
1437 <td>105.74 +/- 8.40</td>
1438 <td>87.14 +/- 3.87</td>
1439 <td>89.08 +/- 1.00</td>
1440 <td>33.53 +/- 2.18</td>
1441 <td>1.05 +/- 0.21</td>
1442 </tr>
1443 <tr>
1444 <td>7</td>
1445 <td>154217</td>
1446 <td>54265 +/- 1588</td>
1447 <td>41680 +/- 5319</td>
1448 <td>224 +/- 18</td>
1449 <td>111.33 +/- 8.90</td>
1450 <td>76.94 +/- 10.52</td>
1451 <td>84.50 +/- 1.41</td>
1452 <td>27.44 +/- 2.33</td>
1453 <td>1.32 +/- 0.25</td>
1454 </tr>
1455 <tr>
1456 <td>8</td>
1457 <td>147969</td>
1458 <td>64363 +/- 2697</td>
1459 <td>39991 +/- 6785</td>
1460 <td>248 +/- 43</td>
1461 <td>109.93 +/- 7.80</td>
1462 <td>62.45 +/- 12.05</td>
1463 <td>82.20 +/- 2.08</td>
1464 <td>24.63 +/- 2.53</td>
1465 <td>1.57 +/- 0.22</td>
1466 </tr>
1467 <tr><td colspan="13">Tile mean across chip</td></tr>
1468 <tr>
1469 <td>Av.</td>
1470 <td></td>
1471 <td>78844</td>
1472 <td>59952</td>
1473 <td>269</td>
1474 <td>103.08</td>
1475 <td>76.79</td>
1476 <td>79.52</td>
1477 <td>23.34</td>
1478 <td>1.06</td>
1479 </tr>
1480 </table>
1481 <h2><br></br>Lane Results Summary : Read 2<br></br></h2>
1482 <table border="1" cellpadding="5">
1483 <tr>
1484 <td colspan="2">Lane Info</td>
1485 <td colspan="8">Tile Mean +/- SD for Lane</td>
1486 </tr>
1487 <tr>
1488 <td>Lane </td>
1489 <td>Lane Yield (kbases) </td>
1490 <td>Clusters (raw)</td>
1491 <td>Clusters (PF) </td>
1492 <td>1st Cycle Int (PF) </td>
1493 <td>% intensity after 20 cycles (PF) </td>
1494 <td>% PF Clusters </td>
1495 <td>% Align (PF) </td>
1496 <td>Alignment Score (PF) </td>
1497 <td> % Error Rate (PF) </td>
1498 </tr>
1499 <tr>
1500 <td>1</td>
1501 <td>277083</td>
1502 <td>103647 +/- 4516</td>
1503 <td>74887 +/- 6080</td>
1504 <td>277 +/- 17</td>
1505 <td>94.42 +/- 5.68</td>
1506 <td>72.22 +/- 4.63</td>
1507 <td>81.54 +/- 2.13</td>
1508 <td>42.70 +/- 5.49</td>
1509 <td>0.89 +/- 0.27</td>
1510 </tr>
1511 <tr>
1512 <td>2</td>
1513 <td>289563</td>
1514 <td>106679 +/- 4653</td>
1515 <td>78260 +/- 2539</td>
1516 <td>259 +/- 13</td>
1517 <td>93.57 +/- 2.55</td>
1518 <td>73.43 +/- 2.52</td>
1519 <td>82.05 +/- 0.37</td>
1520 <td>43.98 +/- 3.02</td>
1521 <td>0.76 +/- 0.15</td>
1522 </tr>
1523 <tr>
1524 <td>3</td>
1525 <td>259242</td>
1526 <td>84584 +/- 5964</td>
1527 <td>70065 +/- 4194</td>
1528 <td>252 +/- 12</td>
1529 <td>94.23 +/- 2.19</td>
1530 <td>82.90 +/- 1.32</td>
1531 <td>84.94 +/- 0.28</td>
1532 <td>51.76 +/- 2.29</td>
1533 <td>0.59 +/- 0.07</td>
1534 </tr>
1535 <tr>
1536 <td>4</td>
1537 <td>210549</td>
1538 <td>68814 +/- 4783</td>
1539 <td>56905 +/- 4145</td>
1540 <td>226 +/- 16</td>
1541 <td>96.82 +/- 7.12</td>
1542 <td>82.91 +/- 5.89</td>
1543 <td>56.01 +/- 0.99</td>
1544 <td>27.86 +/- 3.48</td>
1545 <td>0.95 +/- 0.33</td>
1546 </tr>
1547 <tr>
1548 <td>5</td>
1549 <td>295555</td>
1550 <td>104855 +/- 4665</td>
1551 <td>79879 +/- 6270</td>
1552 <td>200 +/- 24</td>
1553 <td>103.56 +/- 15.45</td>
1554 <td>76.34 +/- 6.67</td>
1555 <td>56.76 +/- 0.41</td>
1556 <td>25.68 +/- 2.06</td>
1557 <td>0.98 +/- 0.17</td>
1558 </tr>
1559 <tr>
1560 <td>6</td>
1561 <td>140401</td>
1562 <td>43556 +/- 1633</td>
1563 <td>37946 +/- 2140</td>
1564 <td>179 +/- 10</td>
1565 <td>100.82 +/- 5.47</td>
1566 <td>87.14 +/- 3.87</td>
1567 <td>88.64 +/- 1.42</td>
1568 <td>34.05 +/- 2.60</td>
1569 <td>0.98 +/- 0.22</td>
1570 </tr>
1571 <tr>
1572 <td>7</td>
1573 <td>154217</td>
1574 <td>54266 +/- 1589</td>
1575 <td>41680 +/- 5319</td>
1576 <td>184 +/- 5</td>
1577 <td>103.42 +/- 3.47</td>
1578 <td>76.94 +/- 10.52</td>
1579 <td>83.90 +/- 1.32</td>
1580 <td>27.60 +/- 2.07</td>
1581 <td>1.26 +/- 0.16</td>
1582 </tr>
1583 <tr>
1584 <td>8</td>
1585 <td>147969</td>
1586 <td>64364 +/- 2698</td>
1587 <td>39991 +/- 6785</td>
1588 <td>206 +/- 31</td>
1589 <td>99.48 +/- 3.23</td>
1590 <td>62.45 +/- 12.05</td>
1591 <td>79.81 +/- 3.35</td>
1592 <td>23.06 +/- 2.50</td>
1593 <td>1.56 +/- 0.23</td>
1594 </tr>
1595 <tr><td colspan="13">Tile mean across chip</td></tr>
1596 <tr>
1597 <td>Av.</td>
1598 <td></td>
1599 <td>78844</td>
1600 <td>59952</td>
1601 <td>223</td>
1602 <td>98.29</td>
1603 <td>76.79</td>
1604 <td>76.70</td>
1605 <td>34.59</td>
1606 <td>1.00</td>
1607 </tr>
1608 </table>
1609 <h2><br></br>Expanded Lane Summary : Read 1<br></br></h2>
1610 <table border="1" cellpadding="5">
1611 <tr>
1612
1613 <tr><td colspan="2">Lane Info</td>
1614 <td colspan="2">Phasing Info</td>
1615 <td colspan="2">Raw Data (tile mean)</td>
1616 <td colspan="7">Filtered Data (tile mean)</td></tr>
1617 <td>Lane </td>
1618 <td>Clusters (tile mean) (raw)</td>
1619 <td>% Phasing </td>
1620 <td>% Prephasing </td>
1621 <td>% Error Rate (raw) </td>
1622 <td> Equiv Perfect Clusters (raw) </td>
1623 <td>% retained </td>
1624 <td>Cycle 2-4 Av Int (PF) </td>
1625 <td>Cycle 2-10 Av % Loss (PF) </td>
1626 <td>Cycle 10-20 Av % Loss (PF) </td>
1627 <td>% Align (PF) </td>
1628 <td>% Error Rate (PF) </td>
1629 <td> Equiv Perfect Clusters (PF) </td>
1630 </tr>
1631 <tr>
1632 <td>1</td>
1633 <td>103646</td>
1634 <td>0.8600</td>
1635 <td>0.4900</td>
1636 <td>1.37</td>
1637 <td>74813</td>
1638 <td>72.22</td>
1639 <td>266 +/- 17</td>
1640 <td>-0.53 +/- 0.37</td>
1641 <td>-0.42 +/- 0.21</td>
1642 <td>89.19</td>
1643 <td>0.94</td>
1644 <td>64718</td>
1645 </tr>
1646 <tr>
1647 <td>2</td>
1648 <td>106678</td>
1649 <td>0.8600</td>
1650 <td>0.4900</td>
1651 <td>1.34</td>
1652 <td>74842</td>
1653 <td>73.43</td>
1654 <td>284 +/- 16</td>
1655 <td>0.08 +/- 0.43</td>
1656 <td>-0.17 +/- 0.34</td>
1657 <td>87.05</td>
1658 <td>0.92</td>
1659 <td>65850</td>
1660 </tr>
1661 <tr>
1662 <td>3</td>
1663 <td>84583</td>
1664 <td>0.8600</td>
1665 <td>0.4900</td>
1666 <td>1.09</td>
1667 <td>65493</td>
1668 <td>82.90</td>
1669 <td>286 +/- 14</td>
1670 <td>0.29 +/- 0.48</td>
1671 <td>-0.02 +/- 0.17</td>
1672 <td>89.49</td>
1673 <td>0.81</td>
1674 <td>60899</td>
1675 </tr>
1676 <tr>
1677 <td>4</td>
1678 <td>68813</td>
1679 <td>0.8600</td>
1680 <td>0.4900</td>
1681 <td>1.19</td>
1682 <td>33697</td>
1683 <td>82.91</td>
1684 <td>286 +/- 23</td>
1685 <td>-0.01 +/- 0.62</td>
1686 <td>-0.37 +/- 0.30</td>
1687 <td>56.93</td>
1688 <td>0.95</td>
1689 <td>31080</td>
1690 </tr>
1691 <tr>
1692 <td>5</td>
1693 <td>104854</td>
1694 <td>0.8600</td>
1695 <td>0.4900</td>
1696 <td>1.32</td>
1697 <td>50075</td>
1698 <td>76.34</td>
1699 <td>258 +/- 25</td>
1700 <td>-0.03 +/- 0.46</td>
1701 <td>-0.49 +/- 0.27</td>
1702 <td>57.71</td>
1703 <td>0.97</td>
1704 <td>44149</td>
1705 </tr>
1706 <tr>
1707 <td>6</td>
1708 <td>43555</td>
1709 <td>0.8600</td>
1710 <td>0.4900</td>
1711 <td>1.24</td>
1712 <td>34399</td>
1713 <td>87.14</td>
1714 <td>231 +/- 14</td>
1715 <td>-0.19 +/- 0.46</td>
1716 <td>-0.34 +/- 0.40</td>
1717 <td>89.08</td>
1718 <td>1.05</td>
1719 <td>32302</td>
1720 </tr>
1721 <tr>
1722 <td>7</td>
1723 <td>54265</td>
1724 <td>0.8600</td>
1725 <td>0.4900</td>
1726 <td>1.67</td>
1727 <td>38188</td>
1728 <td>76.94</td>
1729 <td>224 +/- 14</td>
1730 <td>-0.41 +/- 0.49</td>
1731 <td>-0.55 +/- 0.23</td>
1732 <td>84.50</td>
1733 <td>1.32</td>
1734 <td>33435</td>
1735 </tr>
1736 <tr>
1737 <td>8</td>
1738 <td>64363</td>
1739 <td>0.8600</td>
1740 <td>0.4900</td>
1741 <td>2.15</td>
1742 <td>38077</td>
1743 <td>62.45</td>
1744 <td>247 +/- 42</td>
1745 <td>-0.52 +/- 0.36</td>
1746 <td>-0.29 +/- 0.19</td>
1747 <td>82.20</td>
1748 <td>1.57</td>
1749 <td>31036</td>
1750 </tr>
1751 </table>
1752 <h2><br></br>Expanded Lane Summary : Read 2<br></br></h2>
1753 <table border="1" cellpadding="5">
1754 <tr>
1755
1756 <tr><td colspan="2">Lane Info</td>
1757 <td colspan="2">Phasing Info</td>
1758 <td colspan="2">Raw Data (tile mean)</td>
1759 <td colspan="7">Filtered Data (tile mean)</td></tr>
1760 <td>Lane </td>
1761 <td>Clusters (tile mean) (raw)</td>
1762 <td>% Phasing </td>
1763 <td>% Prephasing </td>
1764 <td>% Error Rate (raw) </td>
1765 <td> Equiv Perfect Clusters (raw) </td>
1766 <td>% retained </td>
1767 <td>Cycle 2-4 Av Int (PF) </td>
1768 <td>Cycle 2-10 Av % Loss (PF) </td>
1769 <td>Cycle 10-20 Av % Loss (PF) </td>
1770 <td>% Align (PF) </td>
1771 <td>% Error Rate (PF) </td>
1772 <td> Equiv Perfect Clusters (PF) </td>
1773 </tr>
1774 <tr>
1775 <td>1</td>
1776 <td>103646</td>
1777 <td>0.7900</td>
1778 <td>0.4600</td>
1779 <td>1.24</td>
1780 <td>68870</td>
1781 <td>72.22</td>
1782 <td>254 +/- 15</td>
1783 <td>-0.53 +/- 0.37</td>
1784 <td>-0.42 +/- 0.21</td>
1785 <td>81.54</td>
1786 <td>0.89</td>
1787 <td>59272</td>
1788 </tr>
1789 <tr>
1790 <td>2</td>
1791 <td>106678</td>
1792 <td>0.7900</td>
1793 <td>0.4600</td>
1794 <td>1.11</td>
1795 <td>71980</td>
1796 <td>73.43</td>
1797 <td>247 +/- 12</td>
1798 <td>0.08 +/- 0.43</td>
1799 <td>-0.17 +/- 0.34</td>
1800 <td>82.05</td>
1801 <td>0.76</td>
1802 <td>62240</td>
1803 </tr>
1804 <tr>
1805 <td>3</td>
1806 <td>84583</td>
1807 <td>0.7900</td>
1808 <td>0.4600</td>
1809 <td>0.80</td>
1810 <td>63500</td>
1811 <td>82.90</td>
1812 <td>243 +/- 8</td>
1813 <td>0.29 +/- 0.48</td>
1814 <td>-0.02 +/- 0.17</td>
1815 <td>84.94</td>
1816 <td>0.59</td>
1817 <td>58029</td>
1818 </tr>
1819 <tr>
1820 <td>4</td>
1821 <td>68813</td>
1822 <td>0.7900</td>
1823 <td>0.4600</td>
1824 <td>1.12</td>
1825 <td>33534</td>
1826 <td>82.91</td>
1827 <td>210 +/- 19</td>
1828 <td>-0.01 +/- 0.62</td>
1829 <td>-0.37 +/- 0.30</td>
1830 <td>56.01</td>
1831 <td>0.95</td>
1832 <td>30548</td>
1833 </tr>
1834 <tr>
1835 <td>5</td>
1836 <td>104854</td>
1837 <td>0.7900</td>
1838 <td>0.4600</td>
1839 <td>1.24</td>
1840 <td>49951</td>
1841 <td>76.34</td>
1842 <td>193 +/- 12</td>
1843 <td>-0.03 +/- 0.46</td>
1844 <td>-0.49 +/- 0.27</td>
1845 <td>56.76</td>
1846 <td>0.98</td>
1847 <td>43366</td>
1848 </tr>
1849 <tr>
1850 <td>6</td>
1851 <td>43555</td>
1852 <td>0.7900</td>
1853 <td>0.4600</td>
1854 <td>1.12</td>
1855 <td>34751</td>
1856 <td>87.14</td>
1857 <td>174 +/- 7</td>
1858 <td>-0.19 +/- 0.46</td>
1859 <td>-0.34 +/- 0.40</td>
1860 <td>88.64</td>
1861 <td>0.98</td>
1862 <td>32208</td>
1863 </tr>
1864 <tr>
1865 <td>7</td>
1866 <td>54265</td>
1867 <td>0.7900</td>
1868 <td>0.4600</td>
1869 <td>1.55</td>
1870 <td>38418</td>
1871 <td>76.94</td>
1872 <td>178 +/- 4</td>
1873 <td>-0.41 +/- 0.49</td>
1874 <td>-0.55 +/- 0.23</td>
1875 <td>83.90</td>
1876 <td>1.26</td>
1877 <td>33240</td>
1878 </tr>
1879 <tr>
1880 <td>8</td>
1881 <td>64363</td>
1882 <td>0.7900</td>
1883 <td>0.4600</td>
1884 <td>2.07</td>
1885 <td>36968</td>
1886 <td>62.45</td>
1887 <td>198 +/- 32</td>
1888 <td>-0.52 +/- 0.36</td>
1889 <td>-0.29 +/- 0.19</td>
1890 <td>79.81</td>
1891 <td>1.56</td>
1892 <td>30181</td>
1893 </tr>
1894 </table>
1895 </body>
1896 </html>"""
1897     pathname = os.path.join(gerald_dir, 'Summary.htm')
1898     f = open(pathname, 'w')
1899     f.write(summary_htm)
1900     f.close()
1901
1902 def make_eland_results(gerald_dir):
1903     eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759    ACATAGNCACAGACATAAACATAGACATAGAC U0      1       1       3       chrUextra.fa    28189829        R       D.
1904 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA  U1      0       1       0       chr2L.fa        8796855 R       DD      24T
1905 >HWI-EAS229_24_207BTAAXX:1:7:776:582    AGCTCANCCGATCGAAAACCTCNCCAAGCAAT        NM      0       0       0
1906 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA        U1      0       1       0       Lambda.fa        8796855 R       DD      24T
1907 """
1908     for i in range(1,9):
1909         pathname = os.path.join(gerald_dir,
1910                                 's_%d_eland_result.txt' % (i,))
1911         f = open(pathname, 'w')
1912         f.write(eland_result)
1913         f.close()
1914
1915 def make_eland_multi(gerald_dir):
1916     eland_multi = """>HWI-EAS229_60_30DP9AAXX:1:1:1221:788   AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT      NM
1917 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:2   chr5.fa:55269838R0
1918 >HWI-EAS229_60_30DP9AAXX:1:1:1121:379   AGAAGAGACATTAAGAGTTCCTGAAATTTATATCTGG   2:1:0   chr16.fa:46189180R1,chr7.fa:122968519R0,chr8.fa:48197174F0
1919 >HWI-EAS229_60_30DP9AAXX:1:1:892:1155   ACATTCTCCTTTCCTTCTGAAGTTTTTACGATTCTTT   0:9:10  chr10.fa:114298201F1,chr12.fa:8125072F1,19500297F2,42341293R2,chr13.fa:27688155R2,95069772R1,chr15.fa:51016475F2,chr16.fa:27052155F2,chr1.fa:192426217R2,chr21.fa:23685310R2,chr2.fa:106680068F1,chr3.fa:185226695F2,chr4.fa:106626808R2,chr5.fa:14704894F1,43530779F1,126543189F2,chr6.fa:74284101F1,chr7.fa:22516603F1,chr9.fa:134886204R
1920 """
1921     for i in range(1,9):
1922         pathname = os.path.join(gerald_dir,
1923                                 's_%d_eland_multi.txt' % (i,))
1924         f = open(pathname, 'w')
1925         f.write(eland_multi)
1926         f.close()