2 Create simulated solexa/illumina runfolders for testing
8 TEST_CODE_DIR = os.path.split(__file__)[0]
9 TESTDATA_DIR = os.path.join(TEST_CODE_DIR, 'testdata')
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)
15 os.mkdir(firecrest_dir)
18 def make_ipar_dir(data_dir, version='1.01'):
20 Construct an artificial ipar parameter file and directory
22 ipar1_01_file = os.path.join(TESTDATA_DIR, 'IPAR1.01.params')
23 shutil.copy(ipar1_01_file, os.path.join(data_dir, '.params'))
25 ipar_dir = os.path.join(data_dir, 'IPAR_%s' % (version,))
26 if not os.path.exists(ipar_dir):
30 def make_flowcell_id(runfolder_dir, flowcell_id=None):
31 if flowcell_id is None:
32 flowcell_id = '207BTAAXY'
34 config = """<?xml version="1.0"?>
37 </FlowcellId>""" % (flowcell_id,)
38 config_dir = os.path.join(runfolder_dir, 'Config')
40 if not os.path.exists(config_dir):
42 pathname = os.path.join(config_dir, 'FlowcellId.xml')
43 f = open(pathname,'w')
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)
52 def make_matrix(matrix_filename):
53 contents = """# Auto-generated frequency response matrix
60 -0.10 -0.10 1.17 -0.03
63 f = open(matrix_filename, 'w')
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>
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)
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)
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)
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)
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)
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)
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
115 pathname = os.path.join(gerald_dir,
116 's_%d_eland_result.txt' % (i,))
117 f = open(pathname, 'w')
118 f.write(eland_result)
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
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])
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])