gaworkflow/pipeline/test/test_runfolder.py

   1 #!/usr/bin/env python
   2
   3 from datetime import datetime, date
   4 import os
   5 import tempfile
   6 import shutil
   7 import unittest
   8
   9 from gaworkflow.pipeline import firecrest
  10 from gaworkflow.pipeline import bustard
  11 from gaworkflow.pipeline import gerald
  12 from gaworkflow.pipeline import runfolder
  13 from gaworkflow.pipeline.runfolder import ElementTree
  14
  15
  16 def make_flowcell_id(runfolder_dir, flowcell_id=None):
  17     if flowcell_id is None:
  18         flowcell_id = '207BTAAXY'
  19
  20     config = """<?xml version="1.0"?>
  21 <FlowcellId>
  22   <Text>%s</Text>
  23 </FlowcellId>""" % (flowcell_id,)
  24     config_dir = os.path.join(runfolder_dir, 'Config')
  25
  26     if not os.path.exists(config_dir):
  27         os.mkdir(config_dir)
  28     pathname = os.path.join(config_dir, 'FlowcellId.xml')
  29     f = open(pathname,'w')
  30     f.write(config)
  31     f.close()
  32
  33 def make_matrix(matrix_dir):
  34     contents = """# Auto-generated frequency response matrix
  35 > A
  36 > C
  37 > G
  38 > T
  39 0.77 0.15 -0.04 -0.04
  40 0.76 1.02 -0.05 -0.06
  41 -0.10 -0.10 1.17 -0.03
  42 -0.13 -0.12 0.80 1.27
  43 """
  44     s_matrix = os.path.join(matrix_dir, 's_matrix.txt')
  45     f = open(s_matrix, 'w')
  46     f.write(contents)
  47     f.close()
  48
  49 def make_phasing_params(bustard_dir):
  50     for lane in range(1,9):
  51         pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
  52         f = open(pathname, 'w')
  53         f.write("""<Parameters>
  54   <Phasing>0.009900</Phasing>
  55   <Prephasing>0.003500</Prephasing>
  56 </Parameters>
  57 """)
  58         f.close()
  59
  60 def make_gerald_config(gerald_dir):
  61     config_xml = """<RunParameters>
  62 <ChipWideRunParameters>
  63   <ANALYSIS>default</ANALYSIS>
  64   <BAD_LANES></BAD_LANES>
  65   <BAD_TILES></BAD_TILES>
  66   <CONTAM_DIR></CONTAM_DIR>
  67   <CONTAM_FILE></CONTAM_FILE>
  68   <ELAND_GENOME>Need_to_specify_ELAND_genome_directory</ELAND_GENOME>
  69   <ELAND_MULTIPLE_INSTANCES>8</ELAND_MULTIPLE_INSTANCES>
  70   <ELAND_REPEAT></ELAND_REPEAT>
  71   <EMAIL_DOMAIN>domain.com</EMAIL_DOMAIN>
  72   <EMAIL_LIST>diane</EMAIL_LIST>
  73   <EMAIL_SERVER>localhost:25</EMAIL_SERVER>
  74   <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>
  75   <EXPT_DIR_ROOT>/home/diane/gec</EXPT_DIR_ROOT>
  76   <FORCE>1</FORCE>
  77   <GENOME_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald/../../Genomes</GENOME_DIR>
  78   <GENOME_FILE>Need_to_specify_genome_file_name</GENOME_FILE>
  79   <HAMSTER_FLAG>genome</HAMSTER_FLAG>
  80   <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>
  81   <POST_RUN_COMMAND></POST_RUN_COMMAND>
  82   <PRB_FILE_SUFFIX>_prb.txt</PRB_FILE_SUFFIX>
  83   <PURE_BASES>12</PURE_BASES>
  84   <QF_PARAMS>'((CHASTITY&gt;=0.6))'</QF_PARAMS>
  85   <QHG_FILE_SUFFIX>_qhg.txt</QHG_FILE_SUFFIX>
  86   <QUALITY_FORMAT>--symbolic</QUALITY_FORMAT>
  87   <READ_LENGTH>32</READ_LENGTH>
  88   <SEQUENCE_FORMAT>--scarf</SEQUENCE_FORMAT>
  89   <SEQ_FILE_SUFFIX>_seq.txt</SEQ_FILE_SUFFIX>
  90   <SIG_FILE_SUFFIX_DEPHASED>_sig2.txt</SIG_FILE_SUFFIX_DEPHASED>
  91   <SIG_FILE_SUFFIX_NOT_DEPHASED>_sig.txt</SIG_FILE_SUFFIX_NOT_DEPHASED>
  92   <SOFTWARE_VERSION>@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp</SOFTWARE_VERSION>
  93   <TILE_REGEX>s_[1-8]_[0-9][0-9][0-9][0-9]</TILE_REGEX>
  94   <TILE_ROOT>s</TILE_ROOT>
  95   <TIME_STAMP>Sat Apr 19 19:08:30 2008</TIME_STAMP>
  96   <TOOLS_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald</TOOLS_DIR>
  97   <USE_BASES>all</USE_BASES>
  98   <WEB_DIR_ROOT>http://host.domain.com/yourshare/</WEB_DIR_ROOT>
  99 </ChipWideRunParameters>
 100 <LaneSpecificRunParameters>
 101   <ANALYSIS>
 102     <s_1>eland</s_1>
 103     <s_2>eland</s_2>
 104     <s_3>eland</s_3>
 105     <s_4>eland</s_4>
 106     <s_5>eland</s_5>
 107     <s_6>eland</s_6>
 108     <s_7>eland</s_7>
 109     <s_8>eland</s_8>
 110   </ANALYSIS>
 111   <ELAND_GENOME>
 112     <s_1>/g/dm3</s_1>
 113     <s_2>/g/equcab1</s_2>
 114     <s_3>/g/equcab1</s_3>
 115     <s_4>/g/canfam2</s_4>
 116     <s_5>/g/hg18</s_5>
 117     <s_6>/g/hg18</s_6>
 118     <s_7>/g/hg18</s_7>
 119     <s_8>/g/hg18</s_8>
 120   </ELAND_GENOME>
 121   <READ_LENGTH>
 122     <s_1>32</s_1>
 123     <s_2>32</s_2>
 124     <s_3>32</s_3>
 125     <s_4>32</s_4>
 126     <s_5>32</s_5>
 127     <s_6>32</s_6>
 128     <s_7>32</s_7>
 129     <s_8>32</s_8>
 130   </READ_LENGTH>
 131   <USE_BASES>
 132     <s_1>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_1>
 133     <s_2>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_2>
 134     <s_3>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_3>
 135     <s_4>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_4>
 136     <s_5>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_5>
 137     <s_6>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_6>
 138     <s_7>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_7>
 139     <s_8>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_8>
 140   </USE_BASES>
 141 </LaneSpecificRunParameters>
 142 </RunParameters>
 143 """
 144     pathname = os.path.join(gerald_dir, 'config.xml')
 145     f = open(pathname,'w')
 146     f.write(config_xml)
 147     f.close()
 148
 149
 150 def make_summary_htm(gerald_dir):
 151     summary_htm = """<!--RUN_TIME Mon Apr 21 11:52:25 2008 -->
 152 <!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.31 2007/03/05 17:52:15 km Exp $-->
 153 <html>
 154 <body>
 155
 156 <a name="Top"><h2><title>080416_HWI-EAS229_0024_207BTAAXX Summary</title></h2></a>
 157 <h1>Summary Information For Experiment 080416_HWI-EAS229_0024_207BTAAXX on Machine HWI-EAS229</h1>
 158 <h2><br></br>Chip Summary<br></br></h2>
 159 <table border="1" cellpadding="5">
 160 <tr><td>Machine</td><td>HWI-EAS229</td></tr>
 161 <tr><td>Run Folder</td><td>080416_HWI-EAS229_0024_207BTAAXX</td></tr>
 162 <tr><td>Chip ID</td><td>unknown</td></tr>
 163 </table>
 164 <h2><br></br>Lane Parameter Summary<br></br></h2>
 165 <table border="1" cellpadding="5">
 166 <tr>
 167 <td>Lane</td>
 168 <td>Sample ID</td>
 169 <td>Sample Target</td>
 170 <td>Sample Type</td>
 171 <td>Length</td>
 172 <td>Filter</td>
 173 <td>Tiles</td>
 174 </tr>
 175 <tr>
 176 <td>1</td>
 177 <td>unknown</td>
 178 <td>dm3</td>
 179 <td>ELAND</td>
 180 <td>32</td>
 181 <td>'((CHASTITY>=0.6))'</td>
 182 <td><a href="#Lane1">Lane 1</a></td>
 183 </tr>
 184 <tr>
 185 <td>2</td>
 186 <td>unknown</td>
 187 <td>equcab1</td>
 188 <td>ELAND</td>
 189 <td>32</td>
 190 <td>'((CHASTITY>=0.6))'</td>
 191 <td><a href="#Lane2">Lane 2</a></td>
 192 </tr>
 193 <tr>
 194 <td>3</td>
 195 <td>unknown</td>
 196 <td>equcab1</td>
 197 <td>ELAND</td>
 198 <td>32</td>
 199 <td>'((CHASTITY>=0.6))'</td>
 200 <td><a href="#Lane3">Lane 3</a></td>
 201 </tr>
 202 <tr>
 203 <td>4</td>
 204 <td>unknown</td>
 205 <td>canfam2</td>
 206 <td>ELAND</td>
 207 <td>32</td>
 208 <td>'((CHASTITY>=0.6))'</td>
 209 <td><a href="#Lane4">Lane 4</a></td>
 210 </tr>
 211 <tr>
 212 <td>5</td>
 213 <td>unknown</td>
 214 <td>hg18</td>
 215 <td>ELAND</td>
 216 <td>32</td>
 217 <td>'((CHASTITY>=0.6))'</td>
 218 <td><a href="#Lane5">Lane 5</a></td>
 219 </tr>
 220 <tr>
 221 <td>6</td>
 222 <td>unknown</td>
 223 <td>hg18</td>
 224 <td>ELAND</td>
 225 <td>32</td>
 226 <td>'((CHASTITY>=0.6))'</td>
 227 <td><a href="#Lane6">Lane 6</a></td>
 228 </tr>
 229 <tr>
 230 <td>7</td>
 231 <td>unknown</td>
 232 <td>hg18</td>
 233 <td>ELAND</td>
 234 <td>32</td>
 235 <td>'((CHASTITY>=0.6))'</td>
 236 <td><a href="#Lane7">Lane 7</a></td>
 237 </tr>
 238 <tr>
 239 <td>8</td>
 240 <td>unknown</td>
 241 <td>hg18</td>
 242 <td>ELAND</td>
 243 <td>32</td>
 244 <td>'((CHASTITY>=0.6))'</td>
 245 <td><a href="#Lane8">Lane 8</a></td>
 246 </tr>
 247 </table>
 248 <h2><br></br>Lane Results Summary<br></br></h2>
 249 <table border="1" cellpadding="5">
 250 <tr>
 251
 252 <td>Lane </td>
 253 <td>Clusters </td>
 254 <td>Av 1st Cycle Int </td>
 255 <td>% intensity after 20 cycles </td>
 256 <td>% PF Clusters </td>
 257 <td>% Align (PF) </td>
 258 <td>Av Alignment Score (PF) </td>
 259 <td> % Error Rate (PF) </td>
 260 </tr>
 261 <tr>
 262 <td>1</td>
 263 <td>17421 +/- 2139</td>
 264 <td>7230 +/- 801</td>
 265 <td>23.73 +/- 10.79</td>
 266 <td>13.00 +/- 22.91</td>
 267 <td>32.03 +/- 18.45</td>
 268 <td>6703.57 +/- 3753.85</td>
 269 <td>4.55 +/- 4.81</td>
 270 </tr>
 271 <tr>
 272 <td>2</td>
 273 <td>20311 +/- 2402</td>
 274 <td>7660 +/- 678</td>
 275 <td>17.03 +/- 4.40</td>
 276 <td>40.74 +/- 30.33</td>
 277 <td>29.54 +/- 9.03</td>
 278 <td>5184.02 +/- 1631.54</td>
 279 <td>3.27 +/- 3.94</td>
 280 </tr>
 281 <tr>
 282 <td>3</td>
 283 <td>20193 +/- 2399</td>
 284 <td>7700 +/- 797</td>
 285 <td>15.75 +/- 3.30</td>
 286 <td>56.56 +/- 17.16</td>
 287 <td>27.33 +/- 7.48</td>
 288 <td>4803.49 +/- 1313.31</td>
 289 <td>3.07 +/- 2.86</td>
 290 </tr>
 291 <tr>
 292 <td>4</td>
 293 <td>15537 +/- 2531</td>
 294 <td>7620 +/- 1392</td>
 295 <td>15.37 +/- 3.79</td>
 296 <td>63.05 +/- 18.30</td>
 297 <td>15.88 +/- 4.99</td>
 298 <td>3162.13 +/- 962.59</td>
 299 <td>3.11 +/- 2.22</td>
 300 </tr>
 301 <tr>
 302 <td>5</td>
 303 <td>32047 +/- 3356</td>
 304 <td>8093 +/- 831</td>
 305 <td>23.79 +/- 6.18</td>
 306 <td>53.36 +/- 18.06</td>
 307 <td>48.04 +/- 13.77</td>
 308 <td>9866.23 +/- 2877.30</td>
 309 <td>2.26 +/- 1.16</td>
 310 </tr>
 311 <tr>
 312 <td>6</td>
 313 <td>32946 +/- 4753</td>
 314 <td>8227 +/- 736</td>
 315 <td>24.07 +/- 4.69</td>
 316 <td>54.65 +/- 12.57</td>
 317 <td>50.98 +/- 10.54</td>
 318 <td>10468.86 +/- 2228.53</td>
 319 <td>2.21 +/- 2.33</td>
 320 </tr>
 321 <tr>
 322 <td>7</td>
 323 <td>39504 +/- 4171</td>
 324 <td>8401 +/- 785</td>
 325 <td>22.55 +/- 4.56</td>
 326 <td>45.22 +/- 10.34</td>
 327 <td>48.41 +/- 9.67</td>
 328 <td>9829.40 +/- 1993.20</td>
 329 <td>2.26 +/- 1.11</td>
 330 </tr>
 331 <tr>
 332 <td>8</td>
 333 <td>37998 +/- 3792</td>
 334 <td>8443 +/- 1211</td>
 335 <td>39.03 +/- 7.52</td>
 336 <td>42.16 +/- 12.35</td>
 337 <td>40.98 +/- 14.89</td>
 338 <td>8128.87 +/- 3055.34</td>
 339 <td>3.57 +/- 2.77</td>
 340 </tr>
 341 </table>
 342 </body>
 343 </html>
 344 """
 345     pathname = os.path.join(gerald_dir, 'Summary.htm')
 346     f = open(pathname, 'w')
 347     f.write(summary_htm)
 348     f.close()
 349
 350 def make_eland_results(gerald_dir):
 351     eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759    ACATAGNCACAGACATAAACATAGACATAGAC U0      1       1       3       chrUextra.fa    28189829        R       D.
 352 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA  U1      0       1       0       chr2L.fa        8796855 R       DD      24T
 353 >HWI-EAS229_24_207BTAAXX:1:7:776:582    AGCTCANCCGATCGAAAACCTCNCCAAGCAAT        NM      0       0       0
 354 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA        U1      0       1       0       Lambda.fa        8796855 R       DD      24T
 355 """
 356     for i in range(1,9):
 357         pathname = os.path.join(gerald_dir,
 358                                 's_%d_eland_result.txt' % (i,))
 359         f = open(pathname, 'w')
 360         f.write(eland_result)
 361         f.close()
 362
 363 class RunfolderTests(unittest.TestCase):
 364     """
 365     Test components of the runfolder processing code
 366     which includes firecrest, bustard, and gerald
 367     """
 368     def setUp(self):
 369         # make a fake runfolder directory
 370         self.temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
 371
 372         self.runfolder_dir = os.path.join(self.temp_dir,
 373                                           '080102_HWI-EAS229_0010_207BTAAXX')
 374         os.mkdir(self.runfolder_dir)
 375
 376         self.data_dir = os.path.join(self.runfolder_dir, 'Data')
 377         os.mkdir(self.data_dir)
 378
 379         self.firecrest_dir = os.path.join(self.data_dir,
 380                                'C1-33_Firecrest1.8.28_12-04-2008_diane'
 381                              )
 382         os.mkdir(self.firecrest_dir)
 383         self.matrix_dir = os.path.join(self.firecrest_dir, 'Matrix')
 384         os.mkdir(self.matrix_dir)
 385         make_matrix(self.matrix_dir)
 386
 387         self.bustard_dir = os.path.join(self.firecrest_dir,
 388                                         'Bustard1.8.28_12-04-2008_diane')
 389         os.mkdir(self.bustard_dir)
 390         make_phasing_params(self.bustard_dir)
 391
 392         self.gerald_dir = os.path.join(self.bustard_dir,
 393                                        'GERALD_12-04-2008_diane')
 394         os.mkdir(self.gerald_dir)
 395         make_gerald_config(self.gerald_dir)
 396         make_summary_htm(self.gerald_dir)
 397         make_eland_results(self.gerald_dir)
 398
 399     def tearDown(self):
 400         shutil.rmtree(self.temp_dir)
 401
 402     def test_firecrest(self):
 403         """
 404         Construct a firecrest object
 405         """
 406         f = firecrest.firecrest(self.firecrest_dir)
 407         self.failUnlessEqual(f.version, '1.8.28')
 408         self.failUnlessEqual(f.start, 1)
 409         self.failUnlessEqual(f.stop, 33)
 410         self.failUnlessEqual(f.user, 'diane')
 411         self.failUnlessEqual(f.date, date(2008,4,12))
 412
 413         xml = f.get_elements()
 414         # just make sure that element tree can serialize the tree
 415         xml_str = ElementTree.tostring(xml)
 416
 417         f2 = firecrest.Firecrest(xml=xml)
 418         self.failUnlessEqual(f.version, f2.version)
 419         self.failUnlessEqual(f.start,   f2.start)
 420         self.failUnlessEqual(f.stop,    f2.stop)
 421         self.failUnlessEqual(f.user,    f2.user)
 422         self.failUnlessEqual(f.date,    f2.date)
 423
 424     def test_bustard(self):
 425         """
 426         construct a bustard object
 427         """
 428         b = bustard.bustard(self.bustard_dir)
 429         self.failUnlessEqual(b.version, '1.8.28')
 430         self.failUnlessEqual(b.date,    date(2008,4,12))
 431         self.failUnlessEqual(b.user,    'diane')
 432         self.failUnlessEqual(len(b.phasing), 8)
 433         self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
 434
 435         xml = b.get_elements()
 436         b2 = bustard.Bustard(xml=xml)
 437         self.failUnlessEqual(b.version, b2.version)
 438         self.failUnlessEqual(b.date,    b2.date )
 439         self.failUnlessEqual(b.user,    b2.user)
 440         self.failUnlessEqual(len(b.phasing), len(b2.phasing))
 441         for key in b.phasing.keys():
 442             self.failUnlessEqual(b.phasing[key].lane,
 443                                  b2.phasing[key].lane)
 444             self.failUnlessEqual(b.phasing[key].phasing,
 445                                  b2.phasing[key].phasing)
 446             self.failUnlessEqual(b.phasing[key].prephasing,
 447                                  b2.phasing[key].prephasing)
 448
 449     def test_gerald(self):
 450         # need to update gerald and make tests for it
 451         g = gerald.gerald(self.gerald_dir)
 452
 453         self.failUnlessEqual(g.version,
 454             '@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp')
 455         self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
 456         self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
 457         self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
 458
 459
 460         # list of genomes, matches what was defined up in
 461         # make_gerald_config.
 462         # the first None is to offset the genomes list to be 1..9
 463         # instead of pythons default 0..8
 464         genomes = [None, '/g/dm3', '/g/equcab1', '/g/equcab1', '/g/canfam2',
 465                          '/g/hg18', '/g/hg18', '/g/hg18', '/g/hg18', ]
 466
 467         # test lane specific parameters from gerald config file
 468         for i in range(1,9):
 469             cur_lane = g.lanes[str(i)]
 470             self.failUnlessEqual(cur_lane.analysis, 'eland')
 471             self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
 472             self.failUnlessEqual(cur_lane.read_length, '32')
 473             self.failUnlessEqual(cur_lane.use_bases, 'Y'*32)
 474
 475         # test data extracted from summary file
 476         clusters = [None,
 477                     (17421, 2139), (20311, 2402), (20193, 2399), (15537, 2531),
 478                     (32047, 3356), (32946, 4753), (39504, 4171), (37998, 3792)]
 479
 480         for i in range(1,9):
 481             summary_lane = g.summary[str(i)]
 482             self.failUnlessEqual(summary_lane.cluster, clusters[i])
 483             self.failUnlessEqual(summary_lane.lane, str(i))
 484
 485         xml = g.get_elements()
 486         # just make sure that element tree can serialize the tree
 487         xml_str = ElementTree.tostring(xml)
 488         g2 = gerald.Gerald(xml=xml)
 489
 490         # do it all again after extracting from the xml file
 491         self.failUnlessEqual(g.version, g2.version)
 492         self.failUnlessEqual(g.date, g2.date)
 493         self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
 494         self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
 495
 496         # test lane specific parameters from gerald config file
 497         for i in range(1,9):
 498             g_lane = g.lanes[str(i)]
 499             g2_lane = g2.lanes[str(i)]
 500             self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
 501             self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
 502             self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
 503             self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
 504
 505         # test (some) summary elements
 506         for i in range(1,9):
 507             g_summary = g.summary[str(i)]
 508             g2_summary = g2.summary[str(i)]
 509             self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
 510             self.failUnlessEqual(g_summary.lane, g2_summary.lane)
 511
 512             g_eland = g.eland_results
 513             g2_eland = g2.eland_results
 514             for lane in g_eland.keys():
 515                 self.failUnlessEqual(g_eland[lane].reads,
 516                                      g2_eland[lane].reads)
 517                 self.failUnlessEqual(len(g_eland[lane].mapped_reads),
 518                                      len(g2_eland[lane].mapped_reads))
 519                 for k in g_eland[lane].mapped_reads.keys():
 520                     self.failUnlessEqual(g_eland[lane].mapped_reads[k],
 521                                          g2_eland[lane].mapped_reads[k])
 522
 523                 self.failUnlessEqual(len(g_eland[lane].match_codes),
 524                                      len(g2_eland[lane].match_codes))
 525                 for k in g_eland[lane].match_codes.keys():
 526                     self.failUnlessEqual(g_eland[lane].match_codes[k],
 527                                          g2_eland[lane].match_codes[k])
 528
 529
 530     def test_eland(self):
 531         dm3_map = { 'chrUextra.fa' : 'dm3/chrUextra.fa',
 532                     'chr2L.fa': 'dm3/chr2L.fa',
 533                     'Lambda.fa': 'Lambda.fa'}
 534         genome_maps = { '1':dm3_map, '2':dm3_map, '3':dm3_map, '4':dm3_map,
 535                         '5':dm3_map, '6':dm3_map, '7':dm3_map, '8':dm3_map }
 536         eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
 537
 538         for i in range(1,9):
 539             lane = eland[str(i)]
 540             self.failUnlessEqual(lane.reads, 4)
 541             self.failUnlessEqual(lane.sample_name, "s")
 542             self.failUnlessEqual(lane.lane_id, unicode(i))
 543             self.failUnlessEqual(len(lane.mapped_reads), 3)
 544             self.failUnlessEqual(lane.mapped_reads['Lambda.fa'], 1)
 545             self.failUnlessEqual(lane.mapped_reads['dm3/chr2L.fa'], 1)
 546             self.failUnlessEqual(lane.match_codes['U1'], 2)
 547             self.failUnlessEqual(lane.match_codes['NM'], 1)
 548
 549         xml = eland.get_elements()
 550         # just make sure that element tree can serialize the tree
 551         xml_str = ElementTree.tostring(xml)
 552         e2 = gerald.ELAND(xml=xml)
 553
 554         for i in range(1,9):
 555             l1 = eland[str(i)]
 556             l2 = e2[str(i)]
 557             self.failUnlessEqual(l1.reads, l2.reads)
 558             self.failUnlessEqual(l1.sample_name, l2.sample_name)
 559             self.failUnlessEqual(l1.lane_id, l2.lane_id)
 560             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
 561             self.failUnlessEqual(len(l1.mapped_reads), 3)
 562             for k in l1.mapped_reads.keys():
 563                 self.failUnlessEqual(l1.mapped_reads[k],
 564                                      l2.mapped_reads[k])
 565
 566             self.failUnlessEqual(len(l1.match_codes), 9)
 567             self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
 568             for k in l1.match_codes.keys():
 569                 self.failUnlessEqual(l1.match_codes[k],
 570                                      l2.match_codes[k])
 571
 572     def test_runfolder(self):
 573         runs = runfolder.get_runs(self.runfolder_dir)
 574
 575         # do we get the flowcell id from the filename?
 576         self.failUnlessEqual(len(runs), 1)
 577         self.failUnlessEqual(runs[0].name, 'run_207BTAAXX_2008-04-19.xml')
 578
 579         # do we get the flowcell id from the FlowcellId.xml file
 580         make_flowcell_id(self.runfolder_dir, '207BTAAXY')
 581         runs = runfolder.get_runs(self.runfolder_dir)
 582         self.failUnlessEqual(len(runs), 1)
 583         self.failUnlessEqual(runs[0].name, 'run_207BTAAXY_2008-04-19.xml')
 584
 585         r1 = runs[0]
 586         xml = r1.get_elements()
 587         xml_str = ElementTree.tostring(xml)
 588
 589         r2 = runfolder.PipelineRun(xml=xml)
 590         self.failUnlessEqual(r1.name, r2.name)
 591         self.failIfEqual(r2.firecrest, None)
 592         self.failIfEqual(r2.bustard, None)
 593         self.failIfEqual(r2.gerald, None)
 594
 595
 596 def suite():
 597     return unittest.makeSuite(RunfolderTests,'test')
 598
 599 if __name__ == "__main__":
 600     unittest.main(defaultTest="suite")
 601