htsworkflow/pipelines/test/simulate_runfolder.py

   1 """
   2 Create simulated solexa/illumina runfolders for testing
   3 """
   4 import gzip
   5 import os
   6 import shutil
   7
   8 TEST_CODE_DIR = os.path.split(__file__)[0]
   9 TESTDATA_DIR = os.path.join(TEST_CODE_DIR, 'testdata')
  10 LANE_LIST = range(1,9)
  11 TILE_LIST = range(1,101)
  12 HISEQ_TILE_LIST = [1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108,
  13                    1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208,
  14                    2101, 2102, 2103, 2104, 2105, 2106, 2107, 2108,
  15                    2201, 2202, 2203, 2204, 2205, 2206, 2207, 2208,]
  16
  17 def make_firecrest_dir(data_dir, version="1.9.2", start=1, stop=37):
  18     firecrest_dir = os.path.join(data_dir,
  19                                  'C%d-%d_Firecrest%s_12-04-2008_diane' % (start, stop, version)
  20                                  )
  21     os.mkdir(firecrest_dir)
  22     return firecrest_dir
  23
  24 def make_ipar_dir(data_dir, version='1.01'):
  25     """
  26     Construct an artificial ipar parameter file and directory
  27     """
  28     ipar1_01_file = os.path.join(TESTDATA_DIR, 'IPAR1.01.params')
  29     shutil.copy(ipar1_01_file, os.path.join(data_dir, '.params'))
  30
  31     ipar_dir = os.path.join(data_dir, 'IPAR_%s' % (version,))
  32     if not os.path.exists(ipar_dir):
  33       os.mkdir(ipar_dir)
  34     return ipar_dir
  35
  36 def make_flowcell_id(runfolder_dir, flowcell_id=None):
  37     if flowcell_id is None:
  38         flowcell_id = '207BTAAXY'
  39
  40     config = """<?xml version="1.0"?>
  41 <FlowcellId>
  42   <Text>%s</Text>
  43 </FlowcellId>""" % (flowcell_id,)
  44     config_dir = os.path.join(runfolder_dir, 'Config')
  45
  46     if not os.path.exists(config_dir):
  47         os.mkdir(config_dir)
  48     pathname = os.path.join(config_dir, 'FlowcellId.xml')
  49     f = open(pathname,'w')
  50     f.write(config)
  51     f.close()
  52
  53 def make_bustard_config132(image_dir):
  54     source = os.path.join(TESTDATA_DIR, 'bustard-config132.xml')
  55     destination = os.path.join(image_dir, 'config.xml')
  56     shutil.copy(source, destination)
  57
  58 def make_aligned_config_1_12(aligned_dir):
  59     """This is rouglhly equivalent to the old gerald file"""
  60     source = os.path.join(TESTDATA_DIR, 'aligned_config_1_12.xml')
  61     destination = os.path.join(aligned_dir, 'config.xml')
  62     shutil.copy(source, destination)
  63
  64 def make_unaligned_config_1_12(unaligned_dir):
  65     demultiplex_pairs = [ # (src,
  66       # dest),
  67         (os.path.join(TESTDATA_DIR, 'demultiplex_1.12.4.2.xml'),
  68          os.path.join(unaligned_dir, 'DemultiplexConfig.xml')),
  69         (os.path.join(TESTDATA_DIR, 'demultiplexed_bustard_1.12.4.2.xml'),
  70          os.path.join(unaligned_dir, 'DemultiplexConfig.xml')),
  71         (os.path.join(TESTDATA_DIR, 'demultiplexed_summary_1.12.4.2.xml'),
  72          os.path.join(unaligned_dir, 'DemultiplexConfig.xml')),
  73     ]
  74     for src, dest in demultiplex_pairs:
  75         shutil.copy(src, dest)
  76
  77 def make_rta_intensities_1460(data_dir, version='1.4.6.0'):
  78     """
  79     Construct an artificial RTA Intensities parameter file and directory
  80     """
  81     intensities_dir = os.path.join(data_dir, 'Intensities')
  82     if not os.path.exists(intensities_dir):
  83       os.mkdir(intensities_dir)
  84
  85     param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config.xml')
  86     shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
  87
  88     return intensities_dir
  89
  90 def make_rta_basecalls_1460(intensities_dir):
  91     """
  92     Construct an artificial RTA Intensities parameter file and directory
  93     """
  94     basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
  95     if not os.path.exists(basecalls_dir):
  96       os.mkdir(basecalls_dir)
  97
  98     param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config.xml')
  99     shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
 100
 101     return basecalls_dir
 102
 103 def make_rta_intensities_1870(data_dir, version='1.8.70.0'):
 104     """
 105     Construct an artificial RTA Intensities parameter file and directory
 106     """
 107     intensities_dir = os.path.join(data_dir, 'Intensities')
 108     if not os.path.exists(intensities_dir):
 109       os.mkdir(intensities_dir)
 110
 111     param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config_1870.xml')
 112     shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
 113
 114     return intensities_dir
 115
 116 def make_rta_intensities_1_10(data_dir, version='1.10.36.0'):
 117     """
 118     Construct an artificial RTA Intensities parameter file and directory
 119     """
 120     intensities_dir = os.path.join(data_dir, 'Intensities')
 121     if not os.path.exists(intensities_dir):
 122       os.mkdir(intensities_dir)
 123
 124     param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config_1.10.xml')
 125     shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
 126
 127     return intensities_dir
 128
 129 def make_rta_intensities_1_12(data_dir, version='1.12.4.2'):
 130     """
 131     Construct an artificial RTA Intensities parameter file and directory
 132     """
 133     intensities_dir = os.path.join(data_dir, 'Intensities')
 134     if not os.path.exists(intensities_dir):
 135       os.mkdir(intensities_dir)
 136
 137     param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config_1.12.4.2.xml')
 138     shutil.copy(param_file, os.path.join(intensities_dir, 'RTAConfig.xml'))
 139
 140     return intensities_dir
 141
 142 def make_rta_basecalls_1870(intensities_dir):
 143     """
 144     Construct an artificial RTA Intensities parameter file and directory
 145     """
 146     basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
 147     if not os.path.exists(basecalls_dir):
 148       os.mkdir(basecalls_dir)
 149
 150     param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config_1870.xml')
 151     shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
 152
 153     return basecalls_dir
 154
 155 def make_rta_basecalls_1_10(intensities_dir):
 156     """
 157     Construct an artificial RTA Intensities parameter file and directory
 158     """
 159     basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
 160     if not os.path.exists(basecalls_dir):
 161         os.mkdir(basecalls_dir)
 162
 163     make_qseqs(basecalls_dir, basecall_info=ABXX_BASE_CALL_INFO)
 164     param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config_1.10.xml')
 165     shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
 166
 167     return basecalls_dir
 168
 169 def make_rta_basecalls_1_12(intensities_dir):
 170     """
 171     Construct an artificial RTA Intensities parameter file and directory
 172     """
 173     basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
 174     if not os.path.exists(basecalls_dir):
 175         os.mkdir(basecalls_dir)
 176
 177     make_qseqs(basecalls_dir, basecall_info=ABXX_BASE_CALL_INFO)
 178     param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config_1.12.4.2.xml')
 179     shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
 180
 181     return basecalls_dir
 182
 183
 184 def make_qseqs(bustard_dir, basecall_info=None):
 185     """
 186     Fill gerald directory with qseq files
 187     """
 188     if basecall_info is None:
 189         qseq_file = '42BRJAAXX_8_1_0039_qseq.txt'
 190         tile_list = TILE_LIST
 191         summary_file = '42BRJAAXX_BustardSummary.xml'
 192     else:
 193         qseq_file = basecall_info.qseq_file
 194         tile_list = basecall_info.tile_list
 195         summary_file = basecall_info.basecall_summary
 196
 197     # 42BRJ 8 1 0039 happened to be a better than usual tile, in that there
 198     # was actually sequence at the start
 199     source = os.path.join(TESTDATA_DIR, qseq_file)
 200     destdir = bustard_dir
 201     if not os.path.isdir(destdir):
 202         os.mkdir(destdir)
 203
 204     for lane in LANE_LIST:
 205         for tile in tile_list:
 206             destination = os.path.join(bustard_dir, 's_%d_1_%04d_qseq.txt' % (lane, tile))
 207             shutil.copy(source, destination)
 208
 209     make_matrix_dir(bustard_dir)
 210     make_phasing_dir(bustard_dir)
 211
 212     summary_source = os.path.join(TESTDATA_DIR, summary_file)
 213     summary_dest = os.path.join(bustard_dir, 'BustardSummary.xml')
 214     shutil.copy(summary_source, summary_dest)
 215
 216     return destdir
 217
 218 def make_scores(gerald_dir, in_temp=True):
 219     """
 220     Fill gerald directory with score temp files
 221     will create the directory if it doesn't exist.
 222     """
 223     source = os.path.join(TESTDATA_DIR, 's_1_0001_score.txt')
 224     destdir = gerald_dir
 225     if in_temp:
 226         destdir = os.path.join(destdir, 'Temp')
 227     if not os.path.isdir(destdir):
 228         os.mkdir(destdir)
 229
 230     for lane in LANE_LIST:
 231         for tile in TILE_LIST:
 232             destination = os.path.join(destdir, 's_%d_%04d_score.txt' % (lane, tile))
 233             shutil.copy(source, destination)
 234
 235     return destdir
 236
 237 def make_matrix_dir(bustard_dir):
 238     """
 239     Create several matrix files in <bustard_dir>/Matrix/
 240
 241     from pipeline 1.4
 242     """
 243     destdir = os.path.join(bustard_dir, 'Matrix')
 244     if not os.path.isdir(destdir):
 245         os.mkdir(destdir)
 246
 247     source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_02_matrix.txt')
 248     for lane in LANE_LIST:
 249         destination = os.path.join(destdir, 's_%d_02_matrix.txt' % ( lane, ))
 250         shutil.copy(source, destination)
 251
 252 def make_matrix(matrix_filename):
 253     contents = """# Auto-generated frequency response matrix
 254 > A
 255 > C
 256 > G
 257 > T
 258 0.77 0.15 -0.04 -0.04
 259 0.76 1.02 -0.05 -0.06
 260 -0.10 -0.10 1.17 -0.03
 261 -0.13 -0.12 0.80 1.27
 262 """
 263     f = open(matrix_filename, 'w')
 264     f.write(contents)
 265     f.close()
 266
 267 def make_matrix_dir_rta160(bustard_dir):
 268     """
 269     Create several matrix files in <bustard_dir>/Matrix/
 270     """
 271     destdir = os.path.join(bustard_dir, 'Matrix')
 272     if not os.path.isdir(destdir):
 273         os.mkdir(destdir)
 274
 275     source = os.path.join(TESTDATA_DIR, '61MMFAAXX_4_1_matrix.txt')
 276     lane_fragments = [ "_%d" % (l,) for l in LANE_LIST]
 277     for fragment in lane_fragments:
 278         destination = os.path.join(destdir, 's%s_1_matrix.txt' % ( fragment, ))
 279         shutil.copy(source, destination)
 280
 281 def make_matrix_dir_rta_1_10(bustard_dir):
 282     make_matrix_dir_rta160(bustard_dir)
 283
 284 def make_matrix_dir_rta_1_12(bustard_dir):
 285     make_matrix_dir_rta160(bustard_dir)
 286
 287 def make_phasing_dir(bustard_dir):
 288     """
 289     Create several phasing files in <bustard_dir>/Phasing/
 290
 291     from pipeline 1.4
 292     """
 293     destdir = os.path.join(bustard_dir, 'Phasing')
 294     if not os.path.isdir(destdir):
 295         os.mkdir(destdir)
 296
 297     source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_01_phasing.xml')
 298     for lane in LANE_LIST:
 299         destination = os.path.join(destdir, 's_%d_01_phasing.xml' % ( lane, ))
 300         shutil.copy(source, destination)
 301
 302 def make_phasing_params(bustard_dir):
 303     for lane in LANE_LIST:
 304         pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
 305         f = open(pathname, 'w')
 306         f.write("""<Parameters>
 307   <Phasing>0.009900</Phasing>
 308   <Prephasing>0.003500</Prephasing>
 309 </Parameters>
 310 """)
 311         f.close()
 312
 313 def make_gerald_config_026(gerald_dir):
 314     source = os.path.join(TESTDATA_DIR, 'gerald_config_0.2.6.xml')
 315     destination = os.path.join(gerald_dir, 'config.xml')
 316     shutil.copy(source, destination)
 317
 318 def make_gerald_config_100(gerald_dir):
 319     source = os.path.join(TESTDATA_DIR, 'gerald_config_1.0.xml')
 320     destination = os.path.join(gerald_dir, 'config.xml')
 321     shutil.copy(source, destination)
 322
 323 def make_gerald_config_1_7(gerald_dir):
 324     """CASAVA 1.7 gerald config"""
 325     source = os.path.join(TESTDATA_DIR, 'gerald_config_1.7.xml')
 326     destination = os.path.join(gerald_dir, 'config.xml')
 327     shutil.copy(source, destination)
 328
 329 def make_summary_htm_100(gerald_dir):
 330     source = os.path.join(TESTDATA_DIR, 'Summary-pipeline100.htm')
 331     destination = os.path.join(gerald_dir, 'Summary.htm')
 332     shutil.copy(source, destination)
 333
 334 def make_summary_htm_110(gerald_dir):
 335     source = os.path.join(TESTDATA_DIR, 'Summary-pipeline110.htm')
 336     destination = os.path.join(gerald_dir, 'Summary.htm')
 337     shutil.copy(source, destination)
 338
 339 def make_summary_paired_htm(gerald_dir):
 340     source = os.path.join(TESTDATA_DIR, 'Summary-paired-pipeline110.htm')
 341     destination = os.path.join(gerald_dir, 'Summary.htm')
 342     shutil.copy(source, destination)
 343
 344 def make_summary_ipar130_htm(gerald_dir):
 345     source = os.path.join(TESTDATA_DIR, 'Summary-ipar130.htm')
 346     destination = os.path.join(gerald_dir, 'Summary.htm')
 347     shutil.copy(source, destination)
 348
 349 def make_summary_rta160_xml(gerald_dir):
 350     source = os.path.join(TESTDATA_DIR, 'Summary-rta160.xml')
 351     destination = os.path.join(gerald_dir, 'Summary.xml')
 352     shutil.copy(source, destination)
 353
 354
 355 def make_summary_casava1_7_xml(gerald_dir):
 356     source = os.path.join(TESTDATA_DIR, 'Summary-casava1.7.xml')
 357     destination = os.path.join(gerald_dir, 'Summary.xml')
 358     shutil.copy(source, destination)
 359
 360
 361 def make_eland_results(gerald_dir):
 362     eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759    ACATAGNCACAGACATAAACATAGACATAGAC U0      1       1       3       chrUextra.fa    28189829        R       D.
 363 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA  U1      0       1       0       chr2L.fa        8796855 R       DD      24T
 364 >HWI-EAS229_24_207BTAAXX:1:7:776:582    AGCTCANCCGATCGAAAACCTCNCCAAGCAAT        NM      0       0       0
 365 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA        U1      0       1       0       Lambda.fa        8796855 R       DD      24T
 366 """
 367     for i in LANE_LIST:
 368         pathname = os.path.join(gerald_dir,
 369                                 's_%d_eland_result.txt' % (i,))
 370         f = open(pathname, 'w')
 371         f.write(eland_result)
 372         f.close()
 373
 374 def make_eland_multi(gerald_dir, paired=False, lane_list=LANE_LIST):
 375     eland_multi = [""">HWI-EAS229_60_30DP9AAXX:1:1:1221:788   AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT      NM
 376 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:2   chr5.fa:55269838R0
 377 >HWI-EAS229_60_30DP9AAXX:1:1:1121:379   AGAAGAGACATTAAGAGTTCCTGAAATTTATATCTGG   2:1:0   chr16.fa:46189180R1,chr7.fa:122968519R0,chr8.fa:48197174F0
 378 >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
 379 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample1:55269838R0
 380 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample2:55269838R0
 381 """, """>HWI-EAS229_60_30DP9AAXX:1:1:1221:788   AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT      NM
 382 >HWI-EAS229_60_30DP9AAXX:1:1:1221:788   NNNNNNNNNNNNNNGTGGTATGGCGGTGTCTGGTCGT     QC
 383 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:2   chr5.fa:55269838R0
 384 >HWI-EAS229_60_30DP9AAXX:1:1:1121:379   AGAAGAGACATTAAGAGTTCCTGAAATTTATATCTGG   2:1:0   chr16.fa:46189180R1,chr7.fa:122968519R0,chr8.fa:48197174F0,chr7.fa:22516603F1,chr9.fa:134886204R
 385 >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
 386 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample1:55269838R0
 387 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample2:55269838R0
 388 """]
 389     if paired:
 390         for e in [1,2]:
 391             for i in lane_list:
 392                 pathname = os.path.join(gerald_dir,
 393                                         's_%d_%d_eland_multi.txt' % (i,e))
 394                 f = open(pathname, 'w')
 395                 f.write(eland_multi[e-1])
 396                 f.close()
 397     else:
 398         for i in lane_list:
 399             pathname = os.path.join(gerald_dir,
 400                                     's_%d_eland_multi.txt' % (i,))
 401             f = open(pathname, 'w')
 402             f.write(eland_multi[0])
 403             f.close()
 404
 405 def make_eland_export(gerald_dir, paired=False, lane_list=LANE_LIST):
 406     source = os.path.join(TESTDATA_DIR, 'casava_1.7_export.txt')
 407
 408     for i in lane_list:
 409         destination = os.path.join(gerald_dir,
 410                                    's_%d_export.txt' % (i,))
 411         shutil.copy(source, destination)
 412
 413
 414 def make_scarf(gerald_dir, lane_list=LANE_LIST):
 415     seq = """HWI-EAS229_92_30VNBAAXX:1:1:0:161:NCAATTACACGACGCTAGCCCTAAAGCTATTTCGAGG:E[aaaabb^a\a_^^a[S`ba_WZUXaaaaaaUKPER
 416 HWI-EAS229_92_30VNBAAXX:1:1:0:447:NAGATGCGCATTTGAAGTAGGAGCAAAAGATCAAGGT:EUabaab^baabaaaaaaaa^^Uaaaaa\aaaa__`a
 417 HWI-EAS229_92_30VNBAAXX:1:1:0:1210:NATAGCCTCTATAGAAGCCACTATTATTTTTTTCTTA:EUa`]`baaaaa^XQU^a`S``S_`J_aaaaaabb^V
 418 HWI-EAS229_92_30VNBAAXX:1:1:0:1867:NTGGAGCAGATATAAAAACAGATGGTGACGTTGAAGT:E[^UaaaUaba^aaa^aa^XV\baaLaLaaaaQVXV^
 419 HWI-EAS229_92_30VNBAAXX:1:1:0:1898:NAGCTCGTGTCGTGAGATGTTAGGTTAAGTCCTGCAA:EK_aaaaaaaaaaaUZaaZaXM[aaaXSM\aaZ]URE
 420 """
 421     for l in lane_list:
 422         pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
 423         f = open(pathname,'w')
 424         f.write(seq)
 425         f.close()
 426
 427 def make_fastq(gerald_dir, lane_list=LANE_LIST):
 428     seq = """@HWI-EAS229:1:2:182:712#0/1
 429 AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
 430 +HWI-EAS229:1:2:182:712#0/1
 431 \\bab_bbaabbababbaaa]]D]bb_baabbab\baa
 432 @HWI-EAS229:1:2:198:621#0/1
 433 CCCCCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCCCC
 434 +HWI-EAS229:1:2:198:621#0/1
 435 [aaaaaaa`_`aaaaaaa[`ZDZaaaaaaaaaaaaaa
 436 @HWI-EAS229:1:2:209:1321#0/1
 437 AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
 438 +HWI-EAS229:1:2:209:1321#0/1
 439 _bbbbbaaababaabbbbab]D]aaaaaaaaaaaaaa
 440 """
 441     for l in lane_list:
 442         pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
 443         f = open(pathname,'w')
 444         f.write(seq)
 445         f.close()
 446
 447 UNALIGNED_READS = [1,2]
 448 UNALIGNED_SAMPLES = [ (1, UNALIGNED_READS, '11111', None, None),
 449                       (2, UNALIGNED_READS, '11112', None, None),
 450                       (3, UNALIGNED_READS, '11113', 1, 'ATCACG'),
 451                       (3, UNALIGNED_READS, '11113', 2, 'CGATGT'),
 452                       (3, UNALIGNED_READS, '11113', 3, 'TTAGGC'),
 453                       (4, UNALIGNED_READS, '11114', 6, 'GCCAAT'),
 454                       (5, UNALIGNED_READS, '11115', 1, 'ATCACG'),
 455                       (5, UNALIGNED_READS, '11116', 7, 'ACTTGA'),
 456                       (5, UNALIGNED_READS, '11117', 9, 'GATCAG'),
 457                       (6, UNALIGNED_READS, '11118', 1, 'ATCACG'),
 458                       (7, UNALIGNED_READS, '11119', 2, 'CGATGT'),
 459                       (8, UNALIGNED_READS, '11120', 3, 'TTAGGC'),
 460                       (1, UNALIGNED_READS, None, None, None),
 461                       (2, UNALIGNED_READS, None, None, None),
 462                       (3, UNALIGNED_READS, None, None, None),
 463                       (4, UNALIGNED_READS, None, None, None),
 464                       (5, UNALIGNED_READS, None, None, None)]
 465
 466
 467 def make_aligned_eland_export(aligned_dir, flowcell_id):
 468     summary_source = os.path.join(TESTDATA_DIR, 'sample_summary_1_12.htm')
 469     for lane, read, project_id, index_id, index_seq in UNALIGNED_SAMPLES:
 470         paths = DemultiplexedPaths(aligned_dir,
 471                                    flowcell_id,
 472                                    lane,
 473                                    project_id,
 474                                    index_id,
 475                                    index_seq)
 476         paths.make_sample_dirs()
 477         paths.make_summary_dirs()
 478         summary_dest = os.path.join(paths.summary_dir, 'Sample_Summary.htm')
 479         shutil.copy(summary_source, summary_dest)
 480
 481         body = get_unaligned_sample_export(lane, index_seq)
 482         for split in ['001','002']:
 483             for read in UNALIGNED_READS:
 484                 suffix = 'R{0}_{1}_export.txt.gz'.format(read, split)
 485                 pathname = paths.make_test_filename(suffix)
 486                 stream = gzip.open(pathname, 'w')
 487                 stream.write(body)
 488                 stream.close()
 489
 490
 491 def make_unaligned_fastqs_1_12(unaligned_dir, flowcell_id):
 492     """Create a default mix of unaligned sample files
 493     """
 494     for lane, read, name, index_id, index in UNALIGNED_SAMPLES:
 495         make_unaligned_fastq_sample_1_12(unaligned_dir,
 496                                          flowcell_id,
 497                                          lane,
 498                                          read,
 499                                          name,
 500                                          index_id,
 501                                          index)
 502
 503 def make_unaligned_fastq_sample_1_12(unaligned_dir,
 504                                      flowcell_id,
 505                                      lane,
 506                                      reads,
 507                                      project_id,
 508                                      index_id=None,
 509                                      index_seq=None):
 510
 511     paths = DemultiplexedPaths(unaligned_dir,
 512                                flowcell_id,
 513                                lane,
 514                                project_id,
 515                                index_id,
 516                                index_seq)
 517     paths.make_sample_dirs()
 518
 519     sample_seq = get_unaligned_sample_fastq_data(flowcell_id, lane, index_seq)
 520     for split in ['001','002']:
 521         for read in reads:
 522             suffix = 'R{0}_{1}.fastq.gz'.format(read, split)
 523             pathname = paths.make_test_filename(suffix)
 524             stream = gzip.open(pathname, 'w')
 525             stream.write(sample_seq)
 526             stream.close()
 527
 528     sheetname = os.path.join(paths.sample_dir, 'SampleSheet.csv')
 529     stream = open(sheetname, 'w')
 530     stream.write('FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject'+os.linesep)
 531     template = '{flowcell},{lane},{id},mm9,{index},Sample #{id},N,PR_indexing,Operator,{sample_project}'+os.linesep
 532     stream.write(template.format(flowcell=flowcell_id,
 533                                  lane=lane,
 534                                  id=paths.sample_id,
 535                                  index=paths.index_seq,
 536                                  sample_project=paths.sample_project))
 537     stream.close()
 538
 539
 540 class DemultiplexedPaths(object):
 541     def __init__(self, basedir, flowcell_id, lane, project_id, index_id, index_seq):
 542         if lane not in LANE_LIST:
 543             raise ValueError("Invalid lane ID: {0}".format(lane))
 544         self.basedir = basedir
 545         self.flowcell_id = flowcell_id
 546         self.lane = lane
 547
 548         if project_id is None:
 549             # undetermined
 550             self.index_seq = ''
 551             self.sample_id = 'lane{0}'.format(lane)
 552             self.sample_project = 'Undetermined_indices'
 553             self.rootname = 'lane{lane}_Undetermined_L00{lane}_'.format(
 554                 lane=lane)
 555             self.project_dir = 'Undetermined_indices'
 556             self.sample_dir = 'Sample_lane{lane}'.format(lane=lane)
 557         elif index_seq is None:
 558             self.index_seq = ''
 559             self.sample_id = project_id
 560             self.sample_project = '{project_id}'.format(project_id=project_id)
 561             self.rootname = '{project_id}_NoIndex_L00{lane}_'.format(
 562                 project_id=project_id,
 563                 lane=lane)
 564             self.project_dir = 'Project_' + self.sample_project
 565             self.sample_dir = 'Sample_{project_id}'.format(
 566                 project_id=project_id)
 567         else:
 568             self.index_seq = index_seq
 569             self.sample_id = project_id
 570             self.sample_project = '{project_id}_Index{index_id}'.format(
 571                 project_id=project_id,
 572                 index_id=index_id)
 573             self.rootname = '{project_id}_{index}_L00{lane}_'.format(
 574                 project_id=project_id,
 575                 index=index_seq,
 576                 lane=lane)
 577             self.project_dir = 'Project_' + self.sample_project
 578             self.sample_dir = 'Sample_{project_id}'.format(
 579                 project_id=project_id)
 580
 581         self.project_dir = os.path.join(self.basedir, self.project_dir)
 582         self.sample_dir = os.path.join(self.project_dir, self.sample_dir)
 583         self.summary_dir = 'Summary_Stats_{0}'.format(self.flowcell_id)
 584         self.summary_dir = os.path.join(self.project_dir, self.summary_dir)
 585         print "HI:", self.summary_dir
 586
 587
 588     def make_sample_dirs(self):
 589         if not os.path.isdir(self.project_dir):
 590             os.mkdir(self.project_dir)
 591         if not os.path.isdir(self.sample_dir):
 592             os.mkdir(self.sample_dir)
 593
 594     def make_summary_dirs(self):
 595         print "HI:", self.summary_dir
 596         if not os.path.isdir(self.summary_dir):
 597             os.mkdir(self.summary_dir)
 598
 599     def make_test_filename(self, suffix):
 600         filename = self.rootname + suffix
 601         pathname = os.path.join(self.sample_dir, filename)
 602         return pathname
 603     def dump(self):
 604         print ('index seq: {0}'.format(self.index_seq))
 605
 606         print ('project dir: {0}'.format(self.project_dir))
 607         print ('sample dir: {0}'.format(self.sample_dir))
 608         print ('rootname: {0}'.format(self.rootname))
 609         print ('path: {0}'.format(
 610             os.path.join(self.project_dir,
 611                          self.sample_dir,
 612                          self.rootname+'R1_001.fastq.gz')))
 613
 614
 615 def get_unaligned_sample_fastq_data(flowcell_id, lane, index_seq):
 616     seq = """@HWI-ST0787:101:{flowcell}:{lane}:1101:2416:3469 1:Y:0:{index}
 617 TCCTTCATTCCACCGGAGTCTGTGGAATTCTCGGGTGCCAAGGAACTCCA
 618 +
 619 CCCFFFFFHHHHHJJJJJJJJJIJJJJJJJJJJJJJJJJIIJJIIJJJJJ
 620 @HWI-ST0787:101:{flowcell}:{lane}:1101:2677:3293 1:Y:0:{index}
 621 TGGAAATCCATTGGGGTTTCCCCTGGAATTCTCGGGTGCCAAGGAACTCC
 622 +
 623 @CCFF3BDHHHHHIIIIIHHIIIDIIIGIIIEGIIIIIIIIIIIIIIIHH
 624 @HWI-ST0787:101:{flowcell}:{lane}:1101:2616:3297 1:Y:0:{index}
 625 TAATACTGCCGGGTAATGATGGCTGGAATTCTCGGGTGCCAAGGAACTCC
 626 +
 627 CCCFFFFFHHHHHCGHJJJJJJJJJJJJJJJJJIIJJJJJJJJJIHJJJI
 628 @HWI-ST0787:101:{flowcell}:{lane}:1101:2545:3319 1:N:0:{index}
 629 TCCTTCATTCCACCGGAGTCTGCTGGAATTCTCGGGTGCCAAGGAACTCC
 630 +
 631 CCCFFFFFHHHFHJGIGHIJHIIGHIGIGIGEHFIJJJIHIJHJIIJJIH
 632 """.format(flowcell=flowcell_id, lane=lane, index=index_seq)
 633     return seq
 634
 635 def get_unaligned_sample_export(lane, index_seq):
 636     body = """HWI-ST0787\t102\t{lane}\t1101\t1207\t1993\t{index}\t1\tAANGGATTCGATCCGGCTTAAGAGATGAAAACCGAAAGGGCCGACCGAA\taaBS`ccceg[`ae[dRR_[[SPPPP__ececfYYWaegh^\\ZLLY\\X`\tNM\t\t\t\t\t\t
 637 HWI-ST0787\t102     {lane}       1101    1478    1997    {index}  1       CAAGAACCCCGGGGGGGGGGGGGCAGAGAGGGGGAATTTTTTTTTTGTT       BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB       NM                                                                                      N
 638 HWI-ST0787      102     {lane}       1101    1625    1994    {index}  1       AANAATGCTACAGAGACAAAACAAAACTGATATGAAAGTTGAGAATAAA       \^BS\cccgegg[Q[QQQ[`egdgffbeggfgh^^YcfgfhXaHY^O^c       chrII.fa
 639 """.format(lane=lane, index=index_seq)
 640     return body
 641
 642 def ls_tree(root):
 643     for dirpath, dirnames, filenames in os.walk(root):
 644         for filename in filenames:
 645             print os.path.join(dirpath, filename)
 646
 647
 648 class BaseCallInfo(object):
 649     """Provide customization for how to setup the base call mock data
 650     """
 651     def __init__(self, qseq_file, tile_list, basecall_summary):
 652         self.qseq_file = qseq_file
 653         self.tile_list = tile_list
 654         self.basecall_summary = basecall_summary
 655
 656 # First generation HiSeq Flowcell
 657 ABXX_BASE_CALL_INFO = BaseCallInfo(
 658     qseq_file='AA01CCABXX_8_2_2207_qseq.txt',
 659     tile_list = HISEQ_TILE_LIST,
 660     basecall_summary = 'AA01CCABXX_BustardSummary.xml')