htsworkflow/pipelines/test/simulate_runfolder.py

   1 """
   2 Create simulated solexa/illumina runfolders for testing
   3 """
   4
   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
  13 def make_firecrest_dir(data_dir, version="1.9.2", start=1, stop=37):
  14     firecrest_dir = os.path.join(data_dir,
  15                                  'C%d-%d_Firecrest%s_12-04-2008_diane' % (start, stop, version)
  16                                  )
  17     os.mkdir(firecrest_dir)
  18     return firecrest_dir
  19
  20 def make_ipar_dir(data_dir, version='1.01'):
  21     """
  22     Construct an artificial ipar parameter file and directory
  23     """
  24     ipar1_01_file = os.path.join(TESTDATA_DIR, 'IPAR1.01.params')
  25     shutil.copy(ipar1_01_file, os.path.join(data_dir, '.params'))
  26
  27     ipar_dir = os.path.join(data_dir, 'IPAR_%s' % (version,))
  28     if not os.path.exists(ipar_dir):
  29       os.mkdir(ipar_dir)
  30     return ipar_dir
  31
  32 def make_flowcell_id(runfolder_dir, flowcell_id=None):
  33     if flowcell_id is None:
  34         flowcell_id = '207BTAAXY'
  35
  36     config = """<?xml version="1.0"?>
  37 <FlowcellId>
  38   <Text>%s</Text>
  39 </FlowcellId>""" % (flowcell_id,)
  40     config_dir = os.path.join(runfolder_dir, 'Config')
  41
  42     if not os.path.exists(config_dir):
  43         os.mkdir(config_dir)
  44     pathname = os.path.join(config_dir, 'FlowcellId.xml')
  45     f = open(pathname,'w')
  46     f.write(config)
  47     f.close()
  48
  49 def make_bustard_config132(image_dir):
  50     source = os.path.join(TESTDATA_DIR, 'bustard-config132.xml')
  51     destination = os.path.join(image_dir, 'config.xml')
  52     shutil.copy(source, destination)
  53
  54 def make_rta_intensities_1460(data_dir, version='1.4.6.0'):
  55     """
  56     Construct an artificial RTA Intensities parameter file and directory
  57     """
  58     intensities_dir = os.path.join(data_dir, 'Intensities')
  59     if not os.path.exists(intensities_dir):
  60       os.mkdir(intensities_dir)
  61
  62     param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config.xml')
  63     shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
  64
  65     return intensities_dir
  66
  67 def make_rta_basecalls_1460(intensities_dir):
  68     """
  69     Construct an artificial RTA Intensities parameter file and directory
  70     """
  71     basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
  72     if not os.path.exists(basecalls_dir):
  73       os.mkdir(basecalls_dir)
  74
  75     param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config.xml')
  76     shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
  77
  78     return basecalls_dir
  79
  80 def make_qseqs(bustard_dir, in_temp=True):
  81     """
  82     Fill gerald directory with qseq files
  83     """
  84     # 42BRJ 8 1 0039 happened to be a better than usual tile, in that there
  85     # was actually sequence at the start
  86     source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_1_0039_qseq.txt')
  87     destdir = bustard_dir
  88     if not os.path.isdir(destdir):
  89         os.mkdir(destdir)
  90
  91     for lane in LANE_LIST:
  92         for tile in TILE_LIST:
  93             destination = os.path.join(bustard_dir, 's_%d_1_%04d_qseq.txt' % (lane, tile))
  94             shutil.copy(source, destination)
  95
  96     make_matrix_dir(bustard_dir)
  97     make_phasing_dir(bustard_dir)
  98
  99     summary_source = os.path.join(TESTDATA_DIR, '42BRJAAXX_BustardSummary.xml')
 100     summary_dest = os.path.join(bustard_dir, 'BustardSummary.xml')
 101     shutil.copy(summary_source, summary_dest)
 102
 103     return destdir
 104
 105 def make_scores(gerald_dir, in_temp=True):
 106     """
 107     Fill gerald directory with score temp files
 108     will create the directory if it doesn't exist.
 109     """
 110     source = os.path.join(TESTDATA_DIR, 's_1_0001_score.txt')
 111     destdir = gerald_dir
 112     if in_temp:
 113         destdir = os.path.join(destdir, 'Temp')
 114     if not os.path.isdir(destdir):
 115         os.mkdir(destdir)
 116
 117     for lane in LANE_LIST:
 118         for tile in TILE_LIST:
 119             destination = os.path.join(destdir, 's_%d_%04d_score.txt' % (lane, tile))
 120             shutil.copy(source, destination)
 121
 122     return destdir
 123
 124 def make_matrix_dir(bustard_dir):
 125     """
 126     Create several matrix files in <bustard_dir>/Matrix/
 127
 128     from pipeline 1.4
 129     """
 130     destdir = os.path.join(bustard_dir, 'Matrix')
 131     if not os.path.isdir(destdir):
 132         os.mkdir(destdir)
 133
 134     source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_02_matrix.txt')
 135     for lane in LANE_LIST:
 136         destination = os.path.join(destdir, 's_%d_02_matrix.txt' % ( lane, ))
 137         shutil.copy(source, destination)
 138
 139 def make_matrix(matrix_filename):
 140     contents = """# Auto-generated frequency response matrix
 141 > A
 142 > C
 143 > G
 144 > T
 145 0.77 0.15 -0.04 -0.04
 146 0.76 1.02 -0.05 -0.06
 147 -0.10 -0.10 1.17 -0.03
 148 -0.13 -0.12 0.80 1.27
 149 """
 150     f = open(matrix_filename, 'w')
 151     f.write(contents)
 152     f.close()
 153
 154 def make_phasing_dir(bustard_dir):
 155     """
 156     Create several phasing files in <bustard_dir>/Phasing/
 157
 158     from pipeline 1.4
 159     """
 160     destdir = os.path.join(bustard_dir, 'Phasing')
 161     if not os.path.isdir(destdir):
 162         os.mkdir(destdir)
 163
 164     source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_01_phasing.xml')
 165     for lane in LANE_LIST:
 166         destination = os.path.join(destdir, 's_%d_01_phasing.xml' % ( lane, ))
 167         shutil.copy(source, destination)
 168
 169 def make_phasing_params(bustard_dir):
 170     for lane in LANE_LIST:
 171         pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
 172         f = open(pathname, 'w')
 173         f.write("""<Parameters>
 174   <Phasing>0.009900</Phasing>
 175   <Prephasing>0.003500</Prephasing>
 176 </Parameters>
 177 """)
 178         f.close()
 179
 180 def make_gerald_config_026(gerald_dir):
 181     source = os.path.join(TESTDATA_DIR, 'gerald_config_0.2.6.xml')
 182     destination = os.path.join(gerald_dir, 'config.xml')
 183     shutil.copy(source, destination)
 184
 185 def make_gerald_config_100(gerald_dir):
 186     source = os.path.join(TESTDATA_DIR, 'gerald_config_1.0.xml')
 187     destination = os.path.join(gerald_dir, 'config.xml')
 188     shutil.copy(source, destination)
 189
 190 def make_summary_htm_100(gerald_dir):
 191     source = os.path.join(TESTDATA_DIR, 'Summary-pipeline100.htm')
 192     destination = os.path.join(gerald_dir, 'Summary.htm')
 193     shutil.copy(source, destination)
 194
 195 def make_summary_htm_110(gerald_dir):
 196     source = os.path.join(TESTDATA_DIR, 'Summary-pipeline110.htm')
 197     destination = os.path.join(gerald_dir, 'Summary.htm')
 198     shutil.copy(source, destination)
 199
 200 def make_summary_paired_htm(gerald_dir):
 201     source = os.path.join(TESTDATA_DIR, 'Summary-paired-pipeline110.htm')
 202     destination = os.path.join(gerald_dir, 'Summary.htm')
 203     shutil.copy(source, destination)
 204
 205 def make_summary_ipar130_htm(gerald_dir):
 206     source = os.path.join(TESTDATA_DIR, 'Summary-ipar130.htm')
 207     destination = os.path.join(gerald_dir, 'Summary.htm')
 208     shutil.copy(source, destination)
 209
 210 def make_eland_results(gerald_dir):
 211     eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759    ACATAGNCACAGACATAAACATAGACATAGAC U0      1       1       3       chrUextra.fa    28189829        R       D.
 212 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA  U1      0       1       0       chr2L.fa        8796855 R       DD      24T
 213 >HWI-EAS229_24_207BTAAXX:1:7:776:582    AGCTCANCCGATCGAAAACCTCNCCAAGCAAT        NM      0       0       0
 214 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA        U1      0       1       0       Lambda.fa        8796855 R       DD      24T
 215 """
 216     for i in LANE_LIST:
 217         pathname = os.path.join(gerald_dir,
 218                                 's_%d_eland_result.txt' % (i,))
 219         f = open(pathname, 'w')
 220         f.write(eland_result)
 221         f.close()
 222
 223 def make_eland_multi(gerald_dir, paired=False, lane_list=LANE_LIST):
 224     eland_multi = [""">HWI-EAS229_60_30DP9AAXX:1:1:1221:788   AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT      NM
 225 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:2   chr5.fa:55269838R0
 226 >HWI-EAS229_60_30DP9AAXX:1:1:1121:379   AGAAGAGACATTAAGAGTTCCTGAAATTTATATCTGG   2:1:0   chr16.fa:46189180R1,chr7.fa:122968519R0,chr8.fa:48197174F0
 227 >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
 228 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample1:55269838R0
 229 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample2:55269838R0
 230 """, """>HWI-EAS229_60_30DP9AAXX:1:1:1221:788   AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT      NM
 231 >HWI-EAS229_60_30DP9AAXX:1:1:1221:788   NNNNNNNNNNNNNNGTGGTATGGCGGTGTCTGGTCGT     QC
 232 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:2   chr5.fa:55269838R0
 233 >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
 234 >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
 235 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample1:55269838R0
 236 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample2:55269838R0
 237 """]
 238     if paired:
 239         for e in [1,2]:
 240             for i in lane_list:
 241                 pathname = os.path.join(gerald_dir,
 242                                         's_%d_%d_eland_multi.txt' % (i,e))
 243                 f = open(pathname, 'w')
 244                 f.write(eland_multi[e-1])
 245                 f.close()
 246     else:
 247         for i in lane_list:
 248             pathname = os.path.join(gerald_dir,
 249                                     's_%d_eland_multi.txt' % (i,))
 250             f = open(pathname, 'w')
 251             f.write(eland_multi[0])
 252             f.close()
 253
 254 def make_scarf(gerald_dir, lane_list=LANE_LIST):
 255     seq = """HWI-EAS229_92_30VNBAAXX:1:1:0:161:NCAATTACACGACGCTAGCCCTAAAGCTATTTCGAGG:E[aaaabb^a\a_^^a[S`ba_WZUXaaaaaaUKPER
 256 HWI-EAS229_92_30VNBAAXX:1:1:0:447:NAGATGCGCATTTGAAGTAGGAGCAAAAGATCAAGGT:EUabaab^baabaaaaaaaa^^Uaaaaa\aaaa__`a
 257 HWI-EAS229_92_30VNBAAXX:1:1:0:1210:NATAGCCTCTATAGAAGCCACTATTATTTTTTTCTTA:EUa`]`baaaaa^XQU^a`S``S_`J_aaaaaabb^V
 258 HWI-EAS229_92_30VNBAAXX:1:1:0:1867:NTGGAGCAGATATAAAAACAGATGGTGACGTTGAAGT:E[^UaaaUaba^aaa^aa^XV\baaLaLaaaaQVXV^
 259 HWI-EAS229_92_30VNBAAXX:1:1:0:1898:NAGCTCGTGTCGTGAGATGTTAGGTTAAGTCCTGCAA:EK_aaaaaaaaaaaUZaaZaXM[aaaXSM\aaZ]URE
 260 """
 261     for l in lane_list:
 262         pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
 263         f = open(pathname,'w')
 264         f.write(seq)
 265         f.close()
 266
 267 def make_fastq(gerald_dir, lane_list=LANE_LIST):
 268     seq = """@HWI-EAS229:1:2:182:712#0/1
 269 AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
 270 +HWI-EAS229:1:2:182:712#0/1
 271 \bab_bbaabbababbaaa]]D]bb_baabbab\baa
 272 @HWI-EAS229:1:2:198:621#0/1
 273 CCCCCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCCCC
 274 +HWI-EAS229:1:2:198:621#0/1
 275 [aaaaaaa`_`aaaaaaa[`ZDZaaaaaaaaaaaaaa
 276 @HWI-EAS229:1:2:209:1321#0/1
 277 AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
 278 +HWI-EAS229:1:2:209:1321#0/1
 279 _bbbbbaaababaabbbbab]D]aaaaaaaaaaaaaa
 280 """
 281     for l in lane_list:
 282         pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
 283         f = open(pathname,'w')
 284         f.write(seq)
 285         f.close()
 286
 287