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
  12 def make_firecrest_dir(data_dir, version="1.9.2", start=1, stop=37):
  13     firecrest_dir = os.path.join(data_dir,
  14                                  'C%d-%d_Firecrest%s_12-04-2008_diane' % (start, stop, version)
  15                                  )
  16     os.mkdir(firecrest_dir)
  17     return firecrest_dir
  18
  19 def make_ipar_dir(data_dir, version='1.01'):
  20     """
  21     Construct an artificial ipar parameter file and directory
  22     """
  23     ipar1_01_file = os.path.join(TESTDATA_DIR, 'IPAR1.01.params')
  24     shutil.copy(ipar1_01_file, os.path.join(data_dir, '.params'))
  25
  26     ipar_dir = os.path.join(data_dir, 'IPAR_%s' % (version,))
  27     if not os.path.exists(ipar_dir):
  28       os.mkdir(ipar_dir)
  29     return ipar_dir
  30
  31 def make_flowcell_id(runfolder_dir, flowcell_id=None):
  32     if flowcell_id is None:
  33         flowcell_id = '207BTAAXY'
  34
  35     config = """<?xml version="1.0"?>
  36 <FlowcellId>
  37   <Text>%s</Text>
  38 </FlowcellId>""" % (flowcell_id,)
  39     config_dir = os.path.join(runfolder_dir, 'Config')
  40
  41     if not os.path.exists(config_dir):
  42         os.mkdir(config_dir)
  43     pathname = os.path.join(config_dir, 'FlowcellId.xml')
  44     f = open(pathname,'w')
  45     f.write(config)
  46     f.close()
  47
  48 def make_bustard_config132(gerald_dir):
  49     source = os.path.join(TESTDATA_DIR, 'bustard-config132.xml')
  50     destination = os.path.join(gerald_dir, 'config.xml')
  51     shutil.copy(source, destination)
  52
  53 def make_rta_intensities_1460(data_dir, version='1.4.6.0'):
  54     """
  55     Construct an artificial RTA Intensities parameter file and directory
  56     """
  57     intensities_dir = os.path.join(data_dir, 'Intensities')
  58     if not os.path.exists(intensities_dir):
  59       os.mkdir(intensities_dir)
  60
  61     param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config.xml')
  62     shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
  63
  64     return intensities_dir
  65
  66 def make_rta_basecalls_1460(intensities_dir):
  67     """
  68     Construct an artificial RTA Intensities parameter file and directory
  69     """
  70     basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
  71     if not os.path.exists(basecalls_dir):
  72       os.mkdir(basecalls_dir)
  73
  74     param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config.xml')
  75     shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
  76
  77     return basecalls_dir
  78
  79
  80 def make_matrix(matrix_filename):
  81     contents = """# Auto-generated frequency response matrix
  82 > A
  83 > C
  84 > G
  85 > T
  86 0.77 0.15 -0.04 -0.04
  87 0.76 1.02 -0.05 -0.06
  88 -0.10 -0.10 1.17 -0.03
  89 -0.13 -0.12 0.80 1.27
  90 """
  91     f = open(matrix_filename, 'w')
  92     f.write(contents)
  93     f.close()
  94
  95 def make_phasing_params(bustard_dir):
  96     for lane in range(1,9):
  97         pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
  98         f = open(pathname, 'w')
  99         f.write("""<Parameters>
 100   <Phasing>0.009900</Phasing>
 101   <Prephasing>0.003500</Prephasing>
 102 </Parameters>
 103 """)
 104         f.close()
 105
 106 def make_gerald_config_026(gerald_dir):
 107     source = os.path.join(TESTDATA_DIR, 'gerald_config_0.2.6.xml')
 108     destination = os.path.join(gerald_dir, 'config.xml')
 109     shutil.copy(source, destination)
 110
 111 def make_gerald_config_100(gerald_dir):
 112     source = os.path.join(TESTDATA_DIR, 'gerald_config_1.0.xml')
 113     destination = os.path.join(gerald_dir, 'config.xml')
 114     shutil.copy(source, destination)
 115
 116 def make_summary_htm_100(gerald_dir):
 117     source = os.path.join(TESTDATA_DIR, 'Summary-pipeline100.htm')
 118     destination = os.path.join(gerald_dir, 'Summary.htm')
 119     shutil.copy(source, destination)
 120
 121 def make_summary_htm_110(gerald_dir):
 122     source = os.path.join(TESTDATA_DIR, 'Summary-pipeline110.htm')
 123     destination = os.path.join(gerald_dir, 'Summary.htm')
 124     shutil.copy(source, destination)
 125
 126 def make_summary_paired_htm(gerald_dir):
 127     source = os.path.join(TESTDATA_DIR, 'Summary-paired-pipeline110.htm')
 128     destination = os.path.join(gerald_dir, 'Summary.htm')
 129     shutil.copy(source, destination)
 130
 131 def make_summary_ipar130_htm(gerald_dir):
 132     source = os.path.join(TESTDATA_DIR, 'Summary-ipar130.htm')
 133     destination = os.path.join(gerald_dir, 'Summary.htm')
 134     shutil.copy(source, destination)
 135
 136 def make_eland_results(gerald_dir):
 137     eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759    ACATAGNCACAGACATAAACATAGACATAGAC U0      1       1       3       chrUextra.fa    28189829        R       D.
 138 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA  U1      0       1       0       chr2L.fa        8796855 R       DD      24T
 139 >HWI-EAS229_24_207BTAAXX:1:7:776:582    AGCTCANCCGATCGAAAACCTCNCCAAGCAAT        NM      0       0       0
 140 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA        U1      0       1       0       Lambda.fa        8796855 R       DD      24T
 141 """
 142     for i in range(1,9):
 143         pathname = os.path.join(gerald_dir,
 144                                 's_%d_eland_result.txt' % (i,))
 145         f = open(pathname, 'w')
 146         f.write(eland_result)
 147         f.close()
 148
 149 def make_eland_multi(gerald_dir, paired=False, lane_list=LANE_LIST):
 150     eland_multi = [""">HWI-EAS229_60_30DP9AAXX:1:1:1221:788   AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT      NM
 151 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:2   chr5.fa:55269838R0
 152 >HWI-EAS229_60_30DP9AAXX:1:1:1121:379   AGAAGAGACATTAAGAGTTCCTGAAATTTATATCTGG   2:1:0   chr16.fa:46189180R1,chr7.fa:122968519R0,chr8.fa:48197174F0
 153 >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
 154 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample1:55269838R0
 155 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample2:55269838R0
 156 """, """>HWI-EAS229_60_30DP9AAXX:1:1:1221:788   AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT      NM
 157 >HWI-EAS229_60_30DP9AAXX:1:1:1221:788   NNNNNNNNNNNNNNGTGGTATGGCGGTGTCTGGTCGT     QC
 158 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:2   chr5.fa:55269838R0
 159 >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
 160 >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
 161 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample1:55269838R0
 162 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample2:55269838R0
 163 """]
 164     if paired:
 165         for e in [1,2]:
 166             for i in lane_list:
 167                 pathname = os.path.join(gerald_dir,
 168                                         's_%d_%d_eland_multi.txt' % (i,e))
 169                 f = open(pathname, 'w')
 170                 f.write(eland_multi[e-1])
 171                 f.close()
 172     else:
 173         for i in lane_list:
 174             pathname = os.path.join(gerald_dir,
 175                                     's_%d_eland_multi.txt' % (i,))
 176             f = open(pathname, 'w')
 177             f.write(eland_multi[0])
 178             f.close()
 179
 180 def make_scarf(gerald_dir, lane_list=LANE_LIST):
 181     seq = """HWI-EAS229_92_30VNBAAXX:1:1:0:161:NCAATTACACGACGCTAGCCCTAAAGCTATTTCGAGG:E[aaaabb^a\a_^^a[S`ba_WZUXaaaaaaUKPER
 182 HWI-EAS229_92_30VNBAAXX:1:1:0:447:NAGATGCGCATTTGAAGTAGGAGCAAAAGATCAAGGT:EUabaab^baabaaaaaaaa^^Uaaaaa\aaaa__`a
 183 HWI-EAS229_92_30VNBAAXX:1:1:0:1210:NATAGCCTCTATAGAAGCCACTATTATTTTTTTCTTA:EUa`]`baaaaa^XQU^a`S``S_`J_aaaaaabb^V
 184 HWI-EAS229_92_30VNBAAXX:1:1:0:1867:NTGGAGCAGATATAAAAACAGATGGTGACGTTGAAGT:E[^UaaaUaba^aaa^aa^XV\baaLaLaaaaQVXV^
 185 HWI-EAS229_92_30VNBAAXX:1:1:0:1898:NAGCTCGTGTCGTGAGATGTTAGGTTAAGTCCTGCAA:EK_aaaaaaaaaaaUZaaZaXM[aaaXSM\aaZ]URE
 186 """
 187     for l in lane_list:
 188         pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
 189         f = open(pathname,'w')
 190         f.write(seq)
 191         f.close()
 192
 193 def make_fastq(gerald_dir, lane_list=LANE_LIST):
 194     seq = """@HWI-EAS229:1:2:182:712#0/1
 195 AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
 196 +HWI-EAS229:1:2:182:712#0/1
 197 \bab_bbaabbababbaaa]]D]bb_baabbab\baa
 198 @HWI-EAS229:1:2:198:621#0/1
 199 CCCCCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCCCC
 200 +HWI-EAS229:1:2:198:621#0/1
 201 [aaaaaaa`_`aaaaaaa[`ZDZaaaaaaaaaaaaaa
 202 @HWI-EAS229:1:2:209:1321#0/1
 203 AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
 204 +HWI-EAS229:1:2:209:1321#0/1
 205 _bbbbbaaababaabbbbab]D]aaaaaaaaaaaaaa
 206 """
 207     for l in lane_list:
 208         pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
 209         f = open(pathname,'w')
 210         f.write(seq)
 211         f.close()
 212
 213