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
  11 def make_firecrest_dir(data_dir, version="1.9.2", start=1, stop=37):
  12     firecrest_dir = os.path.join(data_dir,
  13                                  'C%d-%d_Firecrest%s_12-04-2008_diane' % (start, stop, version)
  14                                  )
  15     os.mkdir(firecrest_dir)
  16     return firecrest_dir
  17
  18 def make_ipar_dir(data_dir, version='1.01'):
  19     """
  20     Construct an artificial ipar parameter file and directory
  21     """
  22     ipar1_01_file = os.path.join(TESTDATA_DIR, 'IPAR1.01.params')
  23     shutil.copy(ipar1_01_file, os.path.join(data_dir, '.params'))
  24
  25     ipar_dir = os.path.join(data_dir, 'IPAR_%s' % (version,))
  26     if not os.path.exists(ipar_dir):
  27       os.mkdir(ipar_dir)
  28     return ipar_dir
  29
  30 def make_flowcell_id(runfolder_dir, flowcell_id=None):
  31     if flowcell_id is None:
  32         flowcell_id = '207BTAAXY'
  33
  34     config = """<?xml version="1.0"?>
  35 <FlowcellId>
  36   <Text>%s</Text>
  37 </FlowcellId>""" % (flowcell_id,)
  38     config_dir = os.path.join(runfolder_dir, 'Config')
  39
  40     if not os.path.exists(config_dir):
  41         os.mkdir(config_dir)
  42     pathname = os.path.join(config_dir, 'FlowcellId.xml')
  43     f = open(pathname,'w')
  44     f.write(config)
  45     f.close()
  46
  47 def make_bustard_config132(gerald_dir):
  48     source = os.path.join(TESTDATA_DIR, 'bustard-config132.xml')
  49     destination = os.path.join(gerald_dir, 'config.xml')
  50     shutil.copy(source, destination)
  51
  52 def make_matrix(matrix_filename):
  53     contents = """# Auto-generated frequency response matrix
  54 > A
  55 > C
  56 > G
  57 > T
  58 0.77 0.15 -0.04 -0.04
  59 0.76 1.02 -0.05 -0.06
  60 -0.10 -0.10 1.17 -0.03
  61 -0.13 -0.12 0.80 1.27
  62 """
  63     f = open(matrix_filename, 'w')
  64     f.write(contents)
  65     f.close()
  66
  67 def make_phasing_params(bustard_dir):
  68     for lane in range(1,9):
  69         pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
  70         f = open(pathname, 'w')
  71         f.write("""<Parameters>
  72   <Phasing>0.009900</Phasing>
  73   <Prephasing>0.003500</Prephasing>
  74 </Parameters>
  75 """)
  76         f.close()
  77
  78 def make_gerald_config_026(gerald_dir):
  79     source = os.path.join(TESTDATA_DIR, 'gerald_config_0.2.6.xml')
  80     destination = os.path.join(gerald_dir, 'config.xml')
  81     shutil.copy(source, destination)
  82
  83 def make_gerald_config_100(gerald_dir):
  84     source = os.path.join(TESTDATA_DIR, 'gerald_config_1.0.xml')
  85     destination = os.path.join(gerald_dir, 'config.xml')
  86     shutil.copy(source, destination)
  87
  88 def make_summary_htm_100(gerald_dir):
  89     source = os.path.join(TESTDATA_DIR, 'Summary-pipeline100.htm')
  90     destination = os.path.join(gerald_dir, 'Summary.htm')
  91     shutil.copy(source, destination)
  92
  93 def make_summary_htm_110(gerald_dir):
  94     source = os.path.join(TESTDATA_DIR, 'Summary-pipeline110.htm')
  95     destination = os.path.join(gerald_dir, 'Summary.htm')
  96     shutil.copy(source, destination)
  97
  98 def make_summary_paired_htm(gerald_dir):
  99     source = os.path.join(TESTDATA_DIR, 'Summary-paired-pipeline110.htm')
 100     destination = os.path.join(gerald_dir, 'Summary.htm')
 101     shutil.copy(source, destination)
 102
 103 def make_summary_ipar130_htm(gerald_dir):
 104     source = os.path.join(TESTDATA_DIR, 'Summary-ipar130.htm')
 105     destination = os.path.join(gerald_dir, 'Summary.htm')
 106     shutil.copy(source, destination)
 107
 108 def make_eland_results(gerald_dir):
 109     eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759    ACATAGNCACAGACATAAACATAGACATAGAC U0      1       1       3       chrUextra.fa    28189829        R       D.
 110 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA  U1      0       1       0       chr2L.fa        8796855 R       DD      24T
 111 >HWI-EAS229_24_207BTAAXX:1:7:776:582    AGCTCANCCGATCGAAAACCTCNCCAAGCAAT        NM      0       0       0
 112 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA        U1      0       1       0       Lambda.fa        8796855 R       DD      24T
 113 """
 114     for i in range(1,9):
 115         pathname = os.path.join(gerald_dir,
 116                                 's_%d_eland_result.txt' % (i,))
 117         f = open(pathname, 'w')
 118         f.write(eland_result)
 119         f.close()
 120
 121 def make_eland_multi(gerald_dir, paired=False):
 122     eland_multi = [""">HWI-EAS229_60_30DP9AAXX:1:1:1221:788   AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT      NM
 123 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:2   chr5.fa:55269838R0
 124 >HWI-EAS229_60_30DP9AAXX:1:1:1121:379   AGAAGAGACATTAAGAGTTCCTGAAATTTATATCTGG   2:1:0   chr16.fa:46189180R1,chr7.fa:122968519R0,chr8.fa:48197174F0
 125 >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
 126 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample1:55269838R0
 127 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample2:55269838R0
 128 """, """>HWI-EAS229_60_30DP9AAXX:1:1:1221:788   AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT      NM
 129 >HWI-EAS229_60_30DP9AAXX:1:1:1221:788   NNNNNNNNNNNNNNGTGGTATGGCGGTGTCTGGTCGT     QC
 130 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:2   chr5.fa:55269838R0
 131 >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
 132 >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
 133 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample1:55269838R0
 134 >HWI-EAS229_60_30DP9AAXX:1:1:931:747    AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA   1:0:0   spike.fa/sample2:55269838R0
 135 """]
 136     if paired:
 137         for e in [1,2]:
 138             for i in range(1,9):
 139                 pathname = os.path.join(gerald_dir,
 140                                         's_%d_%d_eland_multi.txt' % (i,e))
 141                 f = open(pathname, 'w')
 142                 f.write(eland_multi[e-1])
 143                 f.close()
 144     else:
 145         for i in range(1,9):
 146             pathname = os.path.join(gerald_dir,
 147                                     's_%d_eland_multi.txt' % (i,))
 148             f = open(pathname, 'w')
 149             f.write(eland_multi[0])
 150             f.close()