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_matrix(matrix_filename):
  54     contents = """# Auto-generated frequency response matrix
  55 > A
  56 > C
  57 > G
  58 > T
  59 0.77 0.15 -0.04 -0.04
  60 0.76 1.02 -0.05 -0.06
  61 -0.10 -0.10 1.17 -0.03
  62 -0.13 -0.12 0.80 1.27
  63 """
  64     f = open(matrix_filename, 'w')
  65     f.write(contents)
  66     f.close()
  67
  68 def make_phasing_params(bustard_dir):
  69     for lane in range(1,9):
  70         pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
  71         f = open(pathname, 'w')
  72         f.write("""<Parameters>
  73   <Phasing>0.009900</Phasing>
  74   <Prephasing>0.003500</Prephasing>
  75 </Parameters>
  76 """)
  77         f.close()
  78
  79 def make_gerald_config_026(gerald_dir):
  80     source = os.path.join(TESTDATA_DIR, 'gerald_config_0.2.6.xml')
  81     destination = os.path.join(gerald_dir, 'config.xml')
  82     shutil.copy(source, destination)
  83
  84 def make_gerald_config_100(gerald_dir):
  85     source = os.path.join(TESTDATA_DIR, 'gerald_config_1.0.xml')
  86     destination = os.path.join(gerald_dir, 'config.xml')
  87     shutil.copy(source, destination)
  88
  89 def make_summary_htm_100(gerald_dir):
  90     source = os.path.join(TESTDATA_DIR, 'Summary-pipeline100.htm')
  91     destination = os.path.join(gerald_dir, 'Summary.htm')
  92     shutil.copy(source, destination)
  93
  94 def make_summary_htm_110(gerald_dir):
  95     source = os.path.join(TESTDATA_DIR, 'Summary-pipeline110.htm')
  96     destination = os.path.join(gerald_dir, 'Summary.htm')
  97     shutil.copy(source, destination)
  98
  99 def make_summary_paired_htm(gerald_dir):
 100     source = os.path.join(TESTDATA_DIR, 'Summary-paired-pipeline110.htm')
 101     destination = os.path.join(gerald_dir, 'Summary.htm')
 102     shutil.copy(source, destination)
 103
 104 def make_summary_ipar130_htm(gerald_dir):
 105     source = os.path.join(TESTDATA_DIR, 'Summary-ipar130.htm')
 106     destination = os.path.join(gerald_dir, 'Summary.htm')
 107     shutil.copy(source, destination)
 108
 109 def make_eland_results(gerald_dir):
 110     eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759    ACATAGNCACAGACATAAACATAGACATAGAC U0      1       1       3       chrUextra.fa    28189829        R       D.
 111 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA  U1      0       1       0       chr2L.fa        8796855 R       DD      24T
 112 >HWI-EAS229_24_207BTAAXX:1:7:776:582    AGCTCANCCGATCGAAAACCTCNCCAAGCAAT        NM      0       0       0
 113 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA        U1      0       1       0       Lambda.fa        8796855 R       DD      24T
 114 """
 115     for i in range(1,9):
 116         pathname = os.path.join(gerald_dir,
 117                                 's_%d_eland_result.txt' % (i,))
 118         f = open(pathname, 'w')
 119         f.write(eland_result)
 120         f.close()
 121
 122 def make_eland_multi(gerald_dir, paired=False, lane_list=LANE_LIST):
 123     eland_multi = [""">HWI-EAS229_60_30DP9AAXX:1:1:1221:788   AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT      NM
 124 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:2   chr5.fa:55269838R0
 125 >HWI-EAS229_60_30DP9AAXX:1:1:1121:379   AGAAGAGACATTAAGAGTTCCTGAAATTTATATCTGG   2:1:0   chr16.fa:46189180R1,chr7.fa:122968519R0,chr8.fa:48197174F0
 126 >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
 127 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample1:55269838R0
 128 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample2:55269838R0
 129 """, """>HWI-EAS229_60_30DP9AAXX:1:1:1221:788   AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT      NM
 130 >HWI-EAS229_60_30DP9AAXX:1:1:1221:788   NNNNNNNNNNNNNNGTGGTATGGCGGTGTCTGGTCGT     QC
 131 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:2   chr5.fa:55269838R0
 132 >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
 133 >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
 134 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample1:55269838R0
 135 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample2:55269838R0
 136 """]
 137     if paired:
 138         for e in [1,2]:
 139             for i in lane_list:
 140                 pathname = os.path.join(gerald_dir,
 141                                         's_%d_%d_eland_multi.txt' % (i,e))
 142                 f = open(pathname, 'w')
 143                 f.write(eland_multi[e-1])
 144                 f.close()
 145     else:
 146         for i in lane_list:
 147             pathname = os.path.join(gerald_dir,
 148                                     's_%d_eland_multi.txt' % (i,))
 149             f = open(pathname, 'w')
 150             f.write(eland_multi[0])
 151             f.close()
 152
 153 def make_scarf(gerald_dir, lane_list=LANE_LIST):
 154     seq = """HWI-EAS229_92_30VNBAAXX:1:1:0:161:NCAATTACACGACGCTAGCCCTAAAGCTATTTCGAGG:E[aaaabb^a\a_^^a[S`ba_WZUXaaaaaaUKPER
 155 HWI-EAS229_92_30VNBAAXX:1:1:0:447:NAGATGCGCATTTGAAGTAGGAGCAAAAGATCAAGGT:EUabaab^baabaaaaaaaa^^Uaaaaa\aaaa__`a
 156 HWI-EAS229_92_30VNBAAXX:1:1:0:1210:NATAGCCTCTATAGAAGCCACTATTATTTTTTTCTTA:EUa`]`baaaaa^XQU^a`S``S_`J_aaaaaabb^V
 157 HWI-EAS229_92_30VNBAAXX:1:1:0:1867:NTGGAGCAGATATAAAAACAGATGGTGACGTTGAAGT:E[^UaaaUaba^aaa^aa^XV\baaLaLaaaaQVXV^
 158 HWI-EAS229_92_30VNBAAXX:1:1:0:1898:NAGCTCGTGTCGTGAGATGTTAGGTTAAGTCCTGCAA:EK_aaaaaaaaaaaUZaaZaXM[aaaXSM\aaZ]URE
 159 """
 160     for l in lane_list:
 161         pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
 162         f = open(pathname,'w')
 163         f.write(seq)
 164         f.close()
 165
 166 def make_fastq(gerald_dir, lane_list=LANE_LIST):
 167     seq = """@HWI-EAS229:1:2:182:712#0/1
 168 AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
 169 +HWI-EAS229:1:2:182:712#0/1
 170 \bab_bbaabbababbaaa]]D]bb_baabbab\baa
 171 @HWI-EAS229:1:2:198:621#0/1
 172 CCCCCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCCCC
 173 +HWI-EAS229:1:2:198:621#0/1
 174 [aaaaaaa`_`aaaaaaa[`ZDZaaaaaaaaaaaaaa
 175 @HWI-EAS229:1:2:209:1321#0/1
 176 AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
 177 +HWI-EAS229:1:2:209:1321#0/1
 178 _bbbbbaaababaabbbbab]D]aaaaaaaaaaaaaa
 179 """
 180     for l in lane_list:
 181         pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
 182         f = open(pathname,'w')
 183         f.write(seq)
 184         f.close()
 185
 186