htsworkflow/pipelines/test/simulate_runfolder.py

   1 """
   2 Create simulated solexa/illumina runfolders for testing
   3 """
   4
   5 import os
   6
   7
   8 def make_ipar_dir(data_dir):
   9     """
  10     Construct an artificial ipar parameter file and directory
  11     """
  12     params = """<?xml version="1.0"?>
  13 <ImageAnalysis>
  14   <Run Name="IPAR_1.01">
  15     <Software Name="IPAR" Version="2.01.192.0" />
  16     <Cycles First="1" Last="37" Number="37" />
  17     <RunParameters>
  18       <ImagingReads Index="1">
  19         <FirstCycle>1</FirstCycle>
  20         <LastCycle>37</LastCycle>
  21         <RunFolder>081021_HWI-EAS229_0063_30HKUAAXX</RunFolder>
  22       </ImagingReads>
  23       <Reads Index="1">
  24         <FirstCycle>1</FirstCycle>
  25         <LastCycle>37</LastCycle>
  26         <RunFolder>081021_HWI-EAS229_0063_30HKUAAXX</RunFolder>
  27       </Reads>
  28       <Compression>gzip</Compression>
  29       <CompressionSuffix>.p.gz</CompressionSuffix>
  30       <Instrument>HWI-EAS229</Instrument>
  31       <RunFolder>081021_HWI-EAS229_0063_30HKUAAXX</RunFolder>
  32     </RunParameters>
  33     <ImageParameters>
  34       <AutoOffsetFlag>1</AutoOffsetFlag>
  35       <Fwhm>2.7</Fwhm>
  36       <RemappingDistance>1.5</RemappingDistance>
  37       <Threshold>4</Threshold>
  38     </ImageParameters>
  39     <TileSelection>
  40       <Lane Index="1">
  41         <Sample>s</Sample>
  42         <TileRange Max="100" Min="1" />
  43       </Lane>
  44       <Lane Index="2">
  45         <Sample>s</Sample>
  46         <TileRange Max="100" Min="1" />
  47       </Lane>
  48       <Lane Index="3">
  49         <Sample>s</Sample>
  50         <TileRange Max="100" Min="1" />
  51       </Lane>
  52       <Lane Index="4">
  53         <Sample>s</Sample>
  54         <TileRange Max="100" Min="1" />
  55       </Lane>
  56       <Lane Index="5">
  57         <Sample>s</Sample>
  58         <TileRange Max="100" Min="1" />
  59       </Lane>
  60       <Lane Index="6">
  61         <Sample>s</Sample>
  62         <TileRange Max="100" Min="1" />
  63       </Lane>
  64       <Lane Index="7">
  65         <Sample>s</Sample>
  66         <TileRange Max="100" Min="1" />
  67       </Lane>
  68       <Lane Index="8">
  69         <Sample>s</Sample>
  70         <TileRange Max="100" Min="1" />
  71       </Lane>
  72     </TileSelection>
  73   </Run>
  74 </ImageAnalysis>
  75 """
  76     f = open(os.path.join(data_dir, '.params'),'w')
  77     f.write(params)
  78     f.close()
  79     ipar_dir = os.path.join(data_dir, 'IPAR_1.01')
  80     if not os.path.exists(ipar_dir):
  81       os.mkdir(ipar_dir)
  82     return ipar_dir
  83
  84 def make_flowcell_id(runfolder_dir, flowcell_id=None):
  85     if flowcell_id is None:
  86         flowcell_id = '207BTAAXY'
  87
  88     config = """<?xml version="1.0"?>
  89 <FlowcellId>
  90   <Text>%s</Text>
  91 </FlowcellId>""" % (flowcell_id,)
  92     config_dir = os.path.join(runfolder_dir, 'Config')
  93
  94     if not os.path.exists(config_dir):
  95         os.mkdir(config_dir)
  96     pathname = os.path.join(config_dir, 'FlowcellId.xml')
  97     f = open(pathname,'w')
  98     f.write(config)
  99     f.close()
 100
 101 def make_matrix(matrix_dir):
 102     contents = """# Auto-generated frequency response matrix
 103 > A
 104 > C
 105 > G
 106 > T
 107 0.77 0.15 -0.04 -0.04
 108 0.76 1.02 -0.05 -0.06
 109 -0.10 -0.10 1.17 -0.03
 110 -0.13 -0.12 0.80 1.27
 111 """
 112     s_matrix = os.path.join(matrix_dir, 's_matrix.txt')
 113     f = open(s_matrix, 'w')
 114     f.write(contents)
 115     f.close()
 116
 117 def make_phasing_params(bustard_dir):
 118     for lane in range(1,9):
 119         pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
 120         f = open(pathname, 'w')
 121         f.write("""<Parameters>
 122   <Phasing>0.009900</Phasing>
 123   <Prephasing>0.003500</Prephasing>
 124 </Parameters>
 125 """)
 126         f.close()
 127
 128 def make_gerald_config(gerald_dir):
 129     config_xml = """<RunParameters>
 130 <ChipWideRunParameters>
 131   <ANALYSIS>default</ANALYSIS>
 132   <BAD_LANES></BAD_LANES>
 133   <BAD_TILES></BAD_TILES>
 134   <CONTAM_DIR></CONTAM_DIR>
 135   <CONTAM_FILE></CONTAM_FILE>
 136   <ELAND_GENOME>Need_to_specify_ELAND_genome_directory</ELAND_GENOME>
 137   <ELAND_MULTIPLE_INSTANCES>8</ELAND_MULTIPLE_INSTANCES>
 138   <ELAND_REPEAT></ELAND_REPEAT>
 139   <EMAIL_DOMAIN>domain.com</EMAIL_DOMAIN>
 140   <EMAIL_LIST>diane</EMAIL_LIST>
 141   <EMAIL_SERVER>localhost:25</EMAIL_SERVER>
 142   <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>
 143   <EXPT_DIR_ROOT>/home/diane/gec</EXPT_DIR_ROOT>
 144   <FORCE>1</FORCE>
 145   <GENOME_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald/../../Genomes</GENOME_DIR>
 146   <GENOME_FILE>Need_to_specify_genome_file_name</GENOME_FILE>
 147   <HAMSTER_FLAG>genome</HAMSTER_FLAG>
 148   <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>
 149   <POST_RUN_COMMAND></POST_RUN_COMMAND>
 150   <PRB_FILE_SUFFIX>_prb.txt</PRB_FILE_SUFFIX>
 151   <PURE_BASES>12</PURE_BASES>
 152   <QF_PARAMS>'((CHASTITY&gt;=0.6))'</QF_PARAMS>
 153   <QHG_FILE_SUFFIX>_qhg.txt</QHG_FILE_SUFFIX>
 154   <QUALITY_FORMAT>--symbolic</QUALITY_FORMAT>
 155   <READ_LENGTH>32</READ_LENGTH>
 156   <SEQUENCE_FORMAT>--scarf</SEQUENCE_FORMAT>
 157   <SEQ_FILE_SUFFIX>_seq.txt</SEQ_FILE_SUFFIX>
 158   <SIG_FILE_SUFFIX_DEPHASED>_sig2.txt</SIG_FILE_SUFFIX_DEPHASED>
 159   <SIG_FILE_SUFFIX_NOT_DEPHASED>_sig.txt</SIG_FILE_SUFFIX_NOT_DEPHASED>
 160   <SOFTWARE_VERSION>@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp</SOFTWARE_VERSION>
 161   <TILE_REGEX>s_[1-8]_[0-9][0-9][0-9][0-9]</TILE_REGEX>
 162   <TILE_ROOT>s</TILE_ROOT>
 163   <TIME_STAMP>Sat Apr 19 19:08:30 2008</TIME_STAMP>
 164   <TOOLS_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald</TOOLS_DIR>
 165   <USE_BASES>all</USE_BASES>
 166   <WEB_DIR_ROOT>http://host.domain.com/yourshare/</WEB_DIR_ROOT>
 167 </ChipWideRunParameters>
 168 <LaneSpecificRunParameters>
 169   <ANALYSIS>
 170     <s_1>eland</s_1>
 171     <s_2>eland</s_2>
 172     <s_3>eland</s_3>
 173     <s_4>eland</s_4>
 174     <s_5>eland</s_5>
 175     <s_6>eland</s_6>
 176     <s_7>eland</s_7>
 177     <s_8>eland</s_8>
 178   </ANALYSIS>
 179   <ELAND_GENOME>
 180     <s_1>/g/dm3</s_1>
 181     <s_2>/g/equcab1</s_2>
 182     <s_3>/g/equcab1</s_3>
 183     <s_4>/g/canfam2</s_4>
 184     <s_5>/g/hg18</s_5>
 185     <s_6>/g/hg18</s_6>
 186     <s_7>/g/hg18</s_7>
 187     <s_8>/g/hg18</s_8>
 188   </ELAND_GENOME>
 189   <READ_LENGTH>
 190     <s_1>32</s_1>
 191     <s_2>32</s_2>
 192     <s_3>32</s_3>
 193     <s_4>32</s_4>
 194     <s_5>32</s_5>
 195     <s_6>32</s_6>
 196     <s_7>32</s_7>
 197     <s_8>32</s_8>
 198   </READ_LENGTH>
 199   <USE_BASES>
 200     <s_1>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_1>
 201     <s_2>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_2>
 202     <s_3>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_3>
 203     <s_4>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_4>
 204     <s_5>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_5>
 205     <s_6>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_6>
 206     <s_7>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_7>
 207     <s_8>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_8>
 208   </USE_BASES>
 209 </LaneSpecificRunParameters>
 210 </RunParameters>
 211 """
 212     pathname = os.path.join(gerald_dir, 'config.xml')
 213     f = open(pathname,'w')
 214     f.write(config_xml)
 215     f.close()
 216
 217 def make_summary100_htm(gerald_dir):
 218     summary_htm="""<!--RUN_TIME Wed Jul  2 06:47:44 2008 -->
 219 <!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.94 2007/12/04 09:59:07 rshaw Exp $-->
 220 <html>
 221 <body>
 222
 223 <a name="Top"><h2><title>080627_HWI-EAS229_0036_3055HAXX Summary</title></h2></a>
 224 <h1>Summary Information For Experiment 080627_HWI-EAS229_0036_3055HAXX on Machine HWI-EAS229</h1>
 225 <h2><br></br>Chip Summary<br></br></h2>
 226 <table border="1" cellpadding="5">
 227 <tr><td>Machine</td><td>HWI-EAS229</td></tr>
 228 <tr><td>Run Folder</td><td>080627_HWI-EAS229_0036_3055HAXX</td></tr>
 229 <tr><td>Chip ID</td><td>unknown</td></tr>
 230 </table>
 231 <h2><br></br>Chip Results Summary<br></br></h2>
 232 <table border="1" cellpadding="5">
 233 <tr>
 234 <td>Clusters</td>
 235 <td>Clusters (PF)</td>
 236 <td>Yield (kbases)</td>
 237 </tr>
 238 <tr><td>80933224</td>
 239 <td>43577803</td>
 240 <td>1133022</td>
 241 </tr>
 242 </table>
 243 <h2><br></br>Lane Parameter Summary<br></br></h2>
 244 <table border="1" cellpadding="5">
 245 <tr>
 246 <td>Lane</td>
 247 <td>Sample ID</td>
 248 <td>Sample Target</td>
 249 <td>Sample Type</td>
 250 <td>Length</td>
 251 <td>Filter</td>
 252 <td>Num Tiles</td>
 253 <td>Tiles</td>
 254 </tr>
 255 <tr>
 256 <td>1</td>
 257 <td>unknown</td>
 258 <td>mm9</td>
 259 <td>ELAND</td>
 260 <td>26</td>
 261 <td>'((CHASTITY>=0.6))'</td>
 262 <td>100</td>
 263 <td><a href="#Lane1">Lane 1</a></td>
 264 </tr>
 265 <tr>
 266 <td>2</td>
 267 <td>unknown</td>
 268 <td>mm9</td>
 269 <td>ELAND</td>
 270 <td>26</td>
 271 <td>'((CHASTITY>=0.6))'</td>
 272 <td>100</td>
 273 <td><a href="#Lane2">Lane 2</a></td>
 274 </tr>
 275 <tr>
 276 <td>3</td>
 277 <td>unknown</td>
 278 <td>mm9</td>
 279 <td>ELAND</td>
 280 <td>26</td>
 281 <td>'((CHASTITY>=0.6))'</td>
 282 <td>100</td>
 283 <td><a href="#Lane3">Lane 3</a></td>
 284 </tr>
 285 <tr>
 286 <td>4</td>
 287 <td>unknown</td>
 288 <td>elegans170</td>
 289 <td>ELAND</td>
 290 <td>26</td>
 291 <td>'((CHASTITY>=0.6))'</td>
 292 <td>100</td>
 293 <td><a href="#Lane4">Lane 4</a></td>
 294 </tr>
 295 <tr>
 296 <td>5</td>
 297 <td>unknown</td>
 298 <td>elegans170</td>
 299 <td>ELAND</td>
 300 <td>26</td>
 301 <td>'((CHASTITY>=0.6))'</td>
 302 <td>100</td>
 303 <td><a href="#Lane5">Lane 5</a></td>
 304 </tr>
 305 <tr>
 306 <td>6</td>
 307 <td>unknown</td>
 308 <td>elegans170</td>
 309 <td>ELAND</td>
 310 <td>26</td>
 311 <td>'((CHASTITY>=0.6))'</td>
 312 <td>100</td>
 313 <td><a href="#Lane6">Lane 6</a></td>
 314 </tr>
 315 <tr>
 316 <td>7</td>
 317 <td>unknown</td>
 318 <td>elegans170</td>
 319 <td>ELAND</td>
 320 <td>26</td>
 321 <td>'((CHASTITY>=0.6))'</td>
 322 <td>100</td>
 323 <td><a href="#Lane7">Lane 7</a></td>
 324 </tr>
 325 <tr>
 326 <td>8</td>
 327 <td>unknown</td>
 328 <td>elegans170</td>
 329 <td>ELAND</td>
 330 <td>26</td>
 331 <td>'((CHASTITY>=0.6))'</td>
 332 <td>100</td>
 333 <td><a href="#Lane8">Lane 8</a></td>
 334 </tr>
 335 </table>
 336 <h2><br></br>Lane Results Summary<br></br></h2>
 337 <table border="1" cellpadding="5">
 338 <tr>
 339 <td colspan="2">Lane Info</td>
 340 <td colspan="8">Tile Mean +/- SD for Lane</td>
 341 </tr>
 342 <tr>
 343 <td>Lane </td>
 344 <td>Lane Yield (kbases) </td>
 345 <td>Clusters (raw)</td>
 346 <td>Clusters (PF) </td>
 347 <td>1st Cycle Int (PF) </td>
 348 <td>% intensity after 20 cycles (PF) </td>
 349 <td>% PF Clusters </td>
 350 <td>% Align (PF) </td>
 351 <td>Alignment Score (PF) </td>
 352 <td> % Error Rate (PF) </td>
 353 </tr>
 354 <tr>
 355 <td>1</td>
 356 <td>158046</td>
 357 <td>96483 +/- 9074</td>
 358 <td>60787 +/- 4240</td>
 359 <td>329 +/- 35</td>
 360 <td>101.88 +/- 6.03</td>
 361 <td>63.21 +/- 3.29</td>
 362 <td>70.33 +/- 0.24</td>
 363 <td>9054.08 +/- 59.16</td>
 364 <td>0.46 +/- 0.18</td>
 365 </tr>
 366 <tr>
 367 <td>2</td>
 368 <td>156564</td>
 369 <td>133738 +/- 7938</td>
 370 <td>60217 +/- 1926</td>
 371 <td>444 +/- 39</td>
 372 <td>92.62 +/- 7.58</td>
 373 <td>45.20 +/- 3.31</td>
 374 <td>51.98 +/- 0.74</td>
 375 <td>6692.04 +/- 92.49</td>
 376 <td>0.46 +/- 0.09</td>
 377 </tr>
 378 <tr>
 379 <td>3</td>
 380 <td>185818</td>
 381 <td>152142 +/- 10002</td>
 382 <td>71468 +/- 2827</td>
 383 <td>366 +/- 36</td>
 384 <td>91.53 +/- 8.66</td>
 385 <td>47.19 +/- 3.80</td>
 386 <td>82.24 +/- 0.44</td>
 387 <td>10598.68 +/- 64.13</td>
 388 <td>0.41 +/- 0.04</td>
 389 </tr>
 390 <tr>
 391 <td>4</td>
 392 <td>34953</td>
 393 <td>15784 +/- 2162</td>
 394 <td>13443 +/- 1728</td>
 395 <td>328 +/- 40</td>
 396 <td>97.53 +/- 9.87</td>
 397 <td>85.29 +/- 1.91</td>
 398 <td>80.02 +/- 0.53</td>
 399 <td>10368.82 +/- 71.08</td>
 400 <td>0.15 +/- 0.05</td>
 401 </tr>
 402 <tr>
 403 <td>5</td>
 404 <td>167936</td>
 405 <td>119735 +/- 8465</td>
 406 <td>64590 +/- 2529</td>
 407 <td>417 +/- 37</td>
 408 <td>88.69 +/- 14.79</td>
 409 <td>54.10 +/- 2.59</td>
 410 <td>76.95 +/- 0.32</td>
 411 <td>9936.47 +/- 65.75</td>
 412 <td>0.28 +/- 0.02</td>
 413 </tr>
 414 <tr>
 415 <td>6</td>
 416 <td>173463</td>
 417 <td>152177 +/- 8146</td>
 418 <td>66716 +/- 2493</td>
 419 <td>372 +/- 39</td>
 420 <td>87.06 +/- 9.86</td>
 421 <td>43.98 +/- 3.12</td>
 422 <td>78.80 +/- 0.43</td>
 423 <td>10162.28 +/- 49.65</td>
 424 <td>0.38 +/- 0.03</td>
 425 </tr>
 426 <tr>
 427 <td>7</td>
 428 <td>149287</td>
 429 <td>84649 +/- 7325</td>
 430 <td>57418 +/- 3617</td>
 431 <td>295 +/- 28</td>
 432 <td>89.40 +/- 8.23</td>
 433 <td>67.97 +/- 1.82</td>
 434 <td>33.38 +/- 0.25</td>
 435 <td>4247.92 +/- 32.37</td>
 436 <td>1.00 +/- 0.03</td>
 437 </tr>
 438 <tr>
 439 <td>8</td>
 440 <td>106953</td>
 441 <td>54622 +/- 4812</td>
 442 <td>41136 +/- 3309</td>
 443 <td>284 +/- 37</td>
 444 <td>90.21 +/- 9.10</td>
 445 <td>75.39 +/- 2.27</td>
 446 <td>48.33 +/- 0.29</td>
 447 <td>6169.21 +/- 169.50</td>
 448 <td>0.86 +/- 1.22</td>
 449 </tr>
 450 <tr><td colspan="13">Tile mean across chip</td></tr>
 451 <tr>
 452 <td>Av.</td>
 453 <td></td>
 454 <td>101166</td>
 455 <td>54472</td>
 456 <td>354</td>
 457 <td>92.36</td>
 458 <td>60.29</td>
 459 <td>65.25</td>
 460 <td>8403.69</td>
 461 <td>0.50</td>
 462 </tr>
 463 </table>
 464 <h2><br></br>Expanded Lane Summary<br></br></h2>
 465 <table border="1" cellpadding="5">
 466 <tr>
 467
 468 <tr><td colspan="2">Lane Info</td>
 469 <td colspan="2">Phasing Info</td>
 470 <td colspan="2">Raw Data (tile mean)</td>
 471 <td colspan="7">Filtered Data (tile mean)</td></tr>
 472 <td>Lane </td>
 473 <td>Clusters (tile mean) (raw)</td>
 474 <td>% Phasing </td>
 475 <td>% Prephasing </td>
 476 <td>% Error Rate (raw) </td>
 477 <td> Equiv Perfect Clusters (raw) </td>
 478 <td>% retained </td>
 479 <td>Cycle 2-4 Av Int (PF) </td>
 480 <td>Cycle 2-10 Av % Loss (PF) </td>
 481 <td>Cycle 10-20 Av % Loss (PF) </td>
 482 <td>% Align (PF) </td>
 483 <td>% Error Rate (PF) </td>
 484 <td> Equiv Perfect Clusters (PF) </td>
 485 </tr>
 486 <tr>
 487 <td>1</td>
 488 <td>96483</td>
 489 <td>0.7700</td>
 490 <td>0.3100</td>
 491 <td>1.00</td>
 492 <td>49676</td>
 493 <td>63.21</td>
 494 <td>317 +/- 32</td>
 495 <td>0.13 +/- 0.44</td>
 496 <td>-1.14 +/- 0.34</td>
 497 <td>70.33</td>
 498 <td>0.46</td>
 499 <td>41758</td>
 500 </tr>
 501 <tr>
 502 <td>2</td>
 503 <td>133738</td>
 504 <td>0.7700</td>
 505 <td>0.3100</td>
 506 <td>1.22</td>
 507 <td>40467</td>
 508 <td>45.20</td>
 509 <td>415 +/- 33</td>
 510 <td>0.29 +/- 0.40</td>
 511 <td>-0.79 +/- 0.35</td>
 512 <td>51.98</td>
 513 <td>0.46</td>
 514 <td>30615</td>
 515 </tr>
 516 <tr>
 517 <td>3</td>
 518 <td>152142</td>
 519 <td>0.7700</td>
 520 <td>0.3100</td>
 521 <td>1.30</td>
 522 <td>78588</td>
 523 <td>47.19</td>
 524 <td>344 +/- 26</td>
 525 <td>0.68 +/- 0.51</td>
 526 <td>-0.77 +/- 0.42</td>
 527 <td>82.24</td>
 528 <td>0.41</td>
 529 <td>57552</td>
 530 </tr>
 531 <tr>
 532 <td>4</td>
 533 <td>15784</td>
 534 <td>0.7700</td>
 535 <td>0.3100</td>
 536 <td>0.29</td>
 537 <td>11095</td>
 538 <td>85.29</td>
 539 <td>306 +/- 34</td>
 540 <td>0.20 +/- 0.69</td>
 541 <td>-1.28 +/- 0.66</td>
 542 <td>80.02</td>
 543 <td>0.15</td>
 544 <td>10671</td>
 545 </tr>
 546 <tr>
 547 <td>5</td>
 548 <td>119735</td>
 549 <td>0.7700</td>
 550 <td>0.3100</td>
 551 <td>0.85</td>
 552 <td>60335</td>
 553 <td>54.10</td>
 554 <td>380 +/- 32</td>
 555 <td>0.34 +/- 0.49</td>
 556 <td>-1.55 +/- 4.69</td>
 557 <td>76.95</td>
 558 <td>0.28</td>
 559 <td>49015</td>
 560 </tr>
 561 <tr>
 562 <td>6</td>
 563 <td>152177</td>
 564 <td>0.7700</td>
 565 <td>0.3100</td>
 566 <td>1.21</td>
 567 <td>70905</td>
 568 <td>43.98</td>
 569 <td>333 +/- 27</td>
 570 <td>0.57 +/- 0.50</td>
 571 <td>-0.91 +/- 0.39</td>
 572 <td>78.80</td>
 573 <td>0.38</td>
 574 <td>51663</td>
 575 </tr>
 576 <tr>
 577 <td>7</td>
 578 <td>84649</td>
 579 <td>0.7700</td>
 580 <td>0.3100</td>
 581 <td>1.38</td>
 582 <td>21069</td>
 583 <td>67.97</td>
 584 <td>272 +/- 20</td>
 585 <td>1.15 +/- 0.52</td>
 586 <td>-0.84 +/- 0.58</td>
 587 <td>33.38</td>
 588 <td>1.00</td>
 589 <td>18265</td>
 590 </tr>
 591 <tr>
 592 <td>8</td>
 593 <td>54622</td>
 594 <td>0.7700</td>
 595 <td>0.3100</td>
 596 <td>1.17</td>
 597 <td>21335</td>
 598 <td>75.39</td>
 599 <td>262 +/- 31</td>
 600 <td>1.10 +/- 0.59</td>
 601 <td>-1.01 +/- 0.47</td>
 602 <td>48.33</td>
 603 <td>0.86</td>
 604 <td>19104</td>
 605 </tr>
 606 </table>
 607 <b><br></br>IVC Plots</b>
 608 <p> <a href='IVC.htm' target="_blank"> IVC.htm
 609  </a></p>
 610 <b><br></br>All Intensity Plots</b>
 611 <p> <a href='All.htm' target="_blank"> All.htm
 612  </a></p>
 613 <b><br></br>Error graphs: </b>
 614 <p> <a href='Error.htm' target="_blank"> Error.htm
 615  </a></p>
 616 <td><a href="#Top">Back to top</a></td>
 617 <a name="Lane1"><h2><br></br>Lane 1<br></br></h2></a>
 618 <table border="1" cellpadding="5">
 619 <tr>
 620 <td>Lane </td>
 621 <td>Tile </td>
 622 <td>Clusters (raw)</td>
 623 <td>Av 1st Cycle Int (PF) </td>
 624 <td>Av % intensity after 20 cycles (PF) </td>
 625 <td>% PF Clusters </td>
 626 <td>% Align (PF) </td>
 627 <td>Av Alignment Score (PF) </td>
 628 <td>% Error Rate (PF) </td>
 629 </tr>
 630 <tr>
 631 <td>1</td>
 632 <td>0001</td>
 633 <td>114972</td>
 634 <td>326.48</td>
 635 <td>94.39</td>
 636 <td>57.44</td>
 637 <td>70.2</td>
 638 <td>9038.6</td>
 639 <td>0.44</td>
 640 </tr>
 641 </table>
 642 <td><a href="#Top">Back to top</a></td>
 643 <a name="Lane2"><h2><br></br>Lane 2<br></br></h2></a>
 644 <table border="1" cellpadding="5">
 645 <tr>
 646 <td>Lane </td>
 647 <td>Tile </td>
 648 <td>Clusters (raw)</td>
 649 <td>Av 1st Cycle Int (PF) </td>
 650 <td>Av % intensity after 20 cycles (PF) </td>
 651 <td>% PF Clusters </td>
 652 <td>% Align (PF) </td>
 653 <td>Av Alignment Score (PF) </td>
 654 <td>% Error Rate (PF) </td>
 655 </tr>
 656 <tr>
 657 <td>2</td>
 658 <td>0001</td>
 659 <td>147793</td>
 660 <td>448.12</td>
 661 <td>83.68</td>
 662 <td>38.57</td>
 663 <td>53.7</td>
 664 <td>6905.4</td>
 665 <td>0.54</td>
 666 </tr>
 667 </table>
 668 <td><a href="#Top">Back to top</a></td>
 669 <a name="Lane3"><h2><br></br>Lane 3<br></br></h2></a>
 670 <table border="1" cellpadding="5">
 671 <tr>
 672 <td>Lane </td>
 673 <td>Tile </td>
 674 <td>Clusters (raw)</td>
 675 <td>Av 1st Cycle Int (PF) </td>
 676 <td>Av % intensity after 20 cycles (PF) </td>
 677 <td>% PF Clusters </td>
 678 <td>% Align (PF) </td>
 679 <td>Av Alignment Score (PF) </td>
 680 <td>% Error Rate (PF) </td>
 681 </tr>
 682 <tr>
 683 <td>3</td>
 684 <td>0001</td>
 685 <td>167904</td>
 686 <td>374.05</td>
 687 <td>86.91</td>
 688 <td>40.36</td>
 689 <td>81.3</td>
 690 <td>10465.0</td>
 691 <td>0.47</td>
 692 </tr>
 693 </table>
 694 <td><a href="#Top">Back to top</a></td>
 695 <a name="Lane4"><h2><br></br>Lane 4<br></br></h2></a>
 696 <table border="1" cellpadding="5">
 697 <tr>
 698 <td>Lane </td>
 699 <td>Tile </td>
 700 <td>Clusters (raw)</td>
 701 <td>Av 1st Cycle Int (PF) </td>
 702 <td>Av % intensity after 20 cycles (PF) </td>
 703 <td>% PF Clusters </td>
 704 <td>% Align (PF) </td>
 705 <td>Av Alignment Score (PF) </td>
 706 <td>% Error Rate (PF) </td>
 707 </tr>
 708 <tr>
 709 <td>4</td>
 710 <td>0001</td>
 711 <td>20308</td>
 712 <td>276.85</td>
 713 <td>92.87</td>
 714 <td>84.26</td>
 715 <td>80.4</td>
 716 <td>10413.8</td>
 717 <td>0.16</td>
 718 </tr>
 719 </table>
 720 <td><a href="#Top">Back to top</a></td>
 721 <a name="Lane5"><h2><br></br>Lane 5<br></br></h2></a>
 722 <table border="1" cellpadding="5">
 723 <tr>
 724 <td>Lane </td>
 725 <td>Tile </td>
 726 <td>Clusters (raw)</td>
 727 <td>Av 1st Cycle Int (PF) </td>
 728 <td>Av % intensity after 20 cycles (PF) </td>
 729 <td>% PF Clusters </td>
 730 <td>% Align (PF) </td>
 731 <td>Av Alignment Score (PF) </td>
 732 <td>% Error Rate (PF) </td>
 733 </tr>
 734 </table>
 735 <td><a href="#Top">Back to top</a></td>
 736 <a name="Lane6"><h2><br></br>Lane 6<br></br></h2></a>
 737 <table border="1" cellpadding="5">
 738 <tr>
 739 <td>Lane </td>
 740 <td>Tile </td>
 741 <td>Clusters (raw)</td>
 742 <td>Av 1st Cycle Int (PF) </td>
 743 <td>Av % intensity after 20 cycles (PF) </td>
 744 <td>% PF Clusters </td>
 745 <td>% Align (PF) </td>
 746 <td>Av Alignment Score (PF) </td>
 747 <td>% Error Rate (PF) </td>
 748 </tr>
 749 <tr>
 750 <td>6</td>
 751 <td>0001</td>
 752 <td>166844</td>
 753 <td>348.12</td>
 754 <td>77.59</td>
 755 <td>38.13</td>
 756 <td>79.7</td>
 757 <td>10264.4</td>
 758 <td>0.44</td>
 759 </tr>
 760 </table>
 761 <td><a href="#Top">Back to top</a></td>
 762 <a name="Lane7"><h2><br></br>Lane 7<br></br></h2></a>
 763 <table border="1" cellpadding="5">
 764 <tr>
 765 <td>Lane </td>
 766 <td>Tile </td>
 767 <td>Clusters (raw)</td>
 768 <td>Av 1st Cycle Int (PF) </td>
 769 <td>Av % intensity after 20 cycles (PF) </td>
 770 <td>% PF Clusters </td>
 771 <td>% Align (PF) </td>
 772 <td>Av Alignment Score (PF) </td>
 773 <td>% Error Rate (PF) </td>
 774 </tr>
 775 <tr>
 776 <td>7</td>
 777 <td>0001</td>
 778 <td>98913</td>
 779 <td>269.90</td>
 780 <td>86.66</td>
 781 <td>64.55</td>
 782 <td>33.2</td>
 783 <td>4217.5</td>
 784 <td>1.02</td>
 785 </tr>
 786 </table>
 787 <td><a href="#Top">Back to top</a></td>
 788 <a name="Lane8"><h2><br></br>Lane 8<br></br></h2></a>
 789 <table border="1" cellpadding="5">
 790 <tr>
 791 <td>Lane </td>
 792 <td>Tile </td>
 793 <td>Clusters (raw)</td>
 794 <td>Av 1st Cycle Int (PF) </td>
 795 <td>Av % intensity after 20 cycles (PF) </td>
 796 <td>% PF Clusters </td>
 797 <td>% Align (PF) </td>
 798 <td>Av Alignment Score (PF) </td>
 799 <td>% Error Rate (PF) </td>
 800 </tr>
 801 <tr>
 802 <td>8</td>
 803 <td>0001</td>
 804 <td>64972</td>
 805 <td>243.60</td>
 806 <td>89.40</td>
 807 <td>73.17</td>
 808 <td>48.3</td>
 809 <td>6182.8</td>
 810 <td>0.71</td>
 811 </tr>
 812 </table>
 813 <td><a href="#Top">Back to top</a></td>
 814 </body>
 815 </html>
 816 """
 817     pathname = os.path.join(gerald_dir, 'Summary.htm')
 818     f = open(pathname, 'w')
 819     f.write(summary_htm)
 820     f.close()
 821
 822 def make_eland_results(gerald_dir):
 823     eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759    ACATAGNCACAGACATAAACATAGACATAGAC U0      1       1       3       chrUextra.fa    28189829        R       D.
 824 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA  U1      0       1       0       chr2L.fa        8796855 R       DD      24T
 825 >HWI-EAS229_24_207BTAAXX:1:7:776:582    AGCTCANCCGATCGAAAACCTCNCCAAGCAAT        NM      0       0       0
 826 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA        U1      0       1       0       Lambda.fa        8796855 R       DD      24T
 827 """
 828     for i in range(1,9):
 829         pathname = os.path.join(gerald_dir,
 830                                 's_%d_eland_result.txt' % (i,))
 831         f = open(pathname, 'w')
 832         f.write(eland_result)
 833         f.close()