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')
10 LANE_LIST = range(1,9)
11 TILE_LIST = range(1,101)
12 HISEQ_TILE_LIST = [1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108,
13 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208,
14 2101, 2102, 2103, 2104, 2105, 2106, 2107, 2108,
15 2201, 2202, 2203, 2204, 2205, 2206, 2207, 2208,]
17 def make_firecrest_dir(data_dir, version="1.9.2", start=1, stop=37):
18 firecrest_dir = os.path.join(data_dir,
19 'C%d-%d_Firecrest%s_12-04-2008_diane' % (start, stop, version)
21 os.mkdir(firecrest_dir)
24 def make_ipar_dir(data_dir, version='1.01'):
26 Construct an artificial ipar parameter file and directory
28 ipar1_01_file = os.path.join(TESTDATA_DIR, 'IPAR1.01.params')
29 shutil.copy(ipar1_01_file, os.path.join(data_dir, '.params'))
31 ipar_dir = os.path.join(data_dir, 'IPAR_%s' % (version,))
32 if not os.path.exists(ipar_dir):
36 def make_flowcell_id(runfolder_dir, flowcell_id=None):
37 if flowcell_id is None:
38 flowcell_id = '207BTAAXY'
40 config = """<?xml version="1.0"?>
43 </FlowcellId>""" % (flowcell_id,)
44 config_dir = os.path.join(runfolder_dir, 'Config')
46 if not os.path.exists(config_dir):
48 pathname = os.path.join(config_dir, 'FlowcellId.xml')
49 f = open(pathname,'w')
53 def make_runinfo(runfolder_dir, flowcell_id):
54 """Simulate a RunInfo.xml file created by >= RTA 1.9
56 xml = '''<?xml version="1.0"?>
57 <RunInfo xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Version="2">
58 <Run Id="{runfolder}" Number="101">
59 <Flowcell>{flowcell}</Flowcell>
60 <Instrument>SN787</Instrument>
63 <Read Number="1" NumCycles="50" IsIndexedRead="N" />
64 <Read Number="2" NumCycles="7" IsIndexedRead="Y" />
66 <FlowcellLayout LaneCount="8" SurfaceCount="2" SwathCount="3" TileCount="8" />
71 path, runfolder = os.path.split(runfolder_dir)
72 runinfo = os.path.join(runfolder_dir, 'RunInfo.xml')
73 stream = open(runinfo, 'w')
74 stream.write(xml.format(runfolder=runfolder, flowcell=flowcell_id))
78 def make_bustard_config132(image_dir):
79 source = os.path.join(TESTDATA_DIR, 'bustard-config132.xml')
80 destination = os.path.join(image_dir, 'config.xml')
81 shutil.copy(source, destination)
83 def make_aligned_config_1_12(aligned_dir):
84 """This is rouglhly equivalent to the old gerald file"""
85 source = os.path.join(TESTDATA_DIR, '1_12', 'aligned_config_1_12.xml')
86 destination = os.path.join(aligned_dir, 'config.xml')
87 shutil.copy(source, destination)
89 def make_unaligned_config_1_12(unaligned_dir):
90 demultiplex_pairs = [ # (src,
92 (os.path.join(TESTDATA_DIR, '1_12', 'demultiplex_1.12.4.2.xml'),
93 os.path.join(unaligned_dir, 'DemultiplexConfig.xml')),
94 (os.path.join(TESTDATA_DIR, '1_12',
95 'demultiplexed_bustard_1.12.4.2.xml'),
96 os.path.join(unaligned_dir, 'DemultiplexedBustardConfig.xml')),
97 (os.path.join(TESTDATA_DIR, '1_12',
98 'demultiplexed_summary_1.12.4.2.xml'),
99 os.path.join(unaligned_dir, 'DemultiplexedBustardSummary.xml')),
101 for src, dest in demultiplex_pairs:
102 shutil.copy(src, dest)
104 def make_unaligned_status_1_12(unaligned_dir, flowcell_id):
105 basecall_status = ['All.htm', 'Demultiplex_Stats.htm', 'IVC.htm']
106 test_data_root = os.path.join(TESTDATA_DIR, '1_12', 'basecall_stats')
107 basecall_stats = os.path.join(unaligned_dir,
108 'Basecall_Stats_{0}'.format(flowcell_id))
109 os.mkdir(basecall_stats)
110 for filename in basecall_status:
111 source = os.path.join(test_data_root, filename)
112 destination = os.path.join(basecall_stats, filename)
113 shutil.copy(source, destination)
115 def make_rta_intensities_1460(data_dir, version='1.4.6.0'):
117 Construct an artificial RTA Intensities parameter file and directory
119 intensities_dir = os.path.join(data_dir, 'Intensities')
120 if not os.path.exists(intensities_dir):
121 os.mkdir(intensities_dir)
123 param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config.xml')
124 shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
126 return intensities_dir
128 def make_rta_basecalls_1460(intensities_dir):
130 Construct an artificial RTA Intensities parameter file and directory
132 basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
133 if not os.path.exists(basecalls_dir):
134 os.mkdir(basecalls_dir)
136 param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config.xml')
137 shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
141 def make_rta_intensities_1870(data_dir, version='1.8.70.0'):
143 Construct an artificial RTA Intensities parameter file and directory
145 intensities_dir = os.path.join(data_dir, 'Intensities')
146 if not os.path.exists(intensities_dir):
147 os.mkdir(intensities_dir)
149 param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config_1870.xml')
150 shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
152 return intensities_dir
154 def make_rta_intensities_1_10(data_dir, version='1.10.36.0'):
156 Construct an artificial RTA Intensities parameter file and directory
158 intensities_dir = os.path.join(data_dir, 'Intensities')
159 if not os.path.exists(intensities_dir):
160 os.mkdir(intensities_dir)
162 param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config_1.10.xml')
163 shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
165 return intensities_dir
167 def make_rta_intensities_1_12(data_dir, version='1.12.4.2'):
169 Construct an artificial RTA Intensities parameter file and directory
171 intensities_dir = os.path.join(data_dir, 'Intensities')
172 if not os.path.exists(intensities_dir):
173 os.mkdir(intensities_dir)
175 param_file = os.path.join(TESTDATA_DIR, '1_12',
176 'rta_intensities_config_1.12.4.2.xml')
177 shutil.copy(param_file, os.path.join(intensities_dir, 'RTAConfig.xml'))
179 return intensities_dir
181 def make_rta_basecalls_1870(intensities_dir):
183 Construct an artificial RTA Intensities parameter file and directory
185 basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
186 if not os.path.exists(basecalls_dir):
187 os.mkdir(basecalls_dir)
189 param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config_1870.xml')
190 shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
194 def make_rta_basecalls_1_10(intensities_dir):
196 Construct an artificial RTA Intensities parameter file and directory
198 basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
199 if not os.path.exists(basecalls_dir):
200 os.mkdir(basecalls_dir)
202 make_qseqs(basecalls_dir, basecall_info=ABXX_BASE_CALL_INFO)
203 param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config_1.10.xml')
204 shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
208 def make_rta_basecalls_1_12(intensities_dir):
210 Construct an artificial RTA Intensities parameter file and directory
212 basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
213 if not os.path.exists(basecalls_dir):
214 os.mkdir(basecalls_dir)
216 make_qseqs(basecalls_dir, basecall_info=ABXX_BASE_CALL_INFO)
217 param_file = os.path.join(TESTDATA_DIR, '1_12',
218 'rta_basecalls_config_1.12.4.2.xml')
219 shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
224 def make_qseqs(bustard_dir, basecall_info=None):
226 Fill gerald directory with qseq files
228 if basecall_info is None:
229 qseq_file = '42BRJAAXX_8_1_0039_qseq.txt'
230 tile_list = TILE_LIST
231 summary_file = '42BRJAAXX_BustardSummary.xml'
233 qseq_file = basecall_info.qseq_file
234 tile_list = basecall_info.tile_list
235 summary_file = basecall_info.basecall_summary
237 # 42BRJ 8 1 0039 happened to be a better than usual tile, in that there
238 # was actually sequence at the start
239 source = os.path.join(TESTDATA_DIR, qseq_file)
240 destdir = bustard_dir
241 if not os.path.isdir(destdir):
244 for lane in LANE_LIST:
245 for tile in tile_list:
246 destination = os.path.join(bustard_dir, 's_%d_1_%04d_qseq.txt' % (lane, tile))
247 shutil.copy(source, destination)
249 make_matrix_dir(bustard_dir)
250 make_phasing_dir(bustard_dir)
252 summary_source = os.path.join(TESTDATA_DIR, summary_file)
253 summary_dest = os.path.join(bustard_dir, 'BustardSummary.xml')
254 shutil.copy(summary_source, summary_dest)
258 def make_scores(gerald_dir, in_temp=True):
260 Fill gerald directory with score temp files
261 will create the directory if it doesn't exist.
263 source = os.path.join(TESTDATA_DIR, 's_1_0001_score.txt')
266 destdir = os.path.join(destdir, 'Temp')
267 if not os.path.isdir(destdir):
270 for lane in LANE_LIST:
271 for tile in TILE_LIST:
272 destination = os.path.join(destdir, 's_%d_%04d_score.txt' % (lane, tile))
273 shutil.copy(source, destination)
277 def make_matrix_dir(bustard_dir):
279 Create several matrix files in <bustard_dir>/Matrix/
283 destdir = os.path.join(bustard_dir, 'Matrix')
284 if not os.path.isdir(destdir):
287 source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_02_matrix.txt')
288 for lane in LANE_LIST:
289 destination = os.path.join(destdir, 's_%d_02_matrix.txt' % ( lane, ))
290 shutil.copy(source, destination)
292 def make_matrix(matrix_filename):
293 contents = """# Auto-generated frequency response matrix
298 0.77 0.15 -0.04 -0.04
299 0.76 1.02 -0.05 -0.06
300 -0.10 -0.10 1.17 -0.03
301 -0.13 -0.12 0.80 1.27
303 f = open(matrix_filename, 'w')
307 def make_matrix_dir_rta160(bustard_dir):
309 Create several matrix files in <bustard_dir>/Matrix/
311 destdir = os.path.join(bustard_dir, 'Matrix')
312 if not os.path.isdir(destdir):
315 source = os.path.join(TESTDATA_DIR, '61MMFAAXX_4_1_matrix.txt')
316 lane_fragments = [ "_%d" % (l,) for l in LANE_LIST]
317 for fragment in lane_fragments:
318 destination = os.path.join(destdir, 's%s_1_matrix.txt' % ( fragment, ))
319 shutil.copy(source, destination)
321 def make_matrix_dir_rta_1_10(bustard_dir):
322 make_matrix_dir_rta160(bustard_dir)
324 def make_matrix_dir_rta_1_12(bustard_dir):
325 make_matrix_dir_rta160(bustard_dir)
327 def make_phasing_dir(bustard_dir):
329 Create several phasing files in <bustard_dir>/Phasing/
333 destdir = os.path.join(bustard_dir, 'Phasing')
334 if not os.path.isdir(destdir):
337 source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_01_phasing.xml')
338 for lane in LANE_LIST:
339 destination = os.path.join(destdir, 's_%d_01_phasing.xml' % ( lane, ))
340 shutil.copy(source, destination)
342 def make_phasing_params(bustard_dir):
343 for lane in LANE_LIST:
344 pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
345 f = open(pathname, 'w')
346 f.write("""<Parameters>
347 <Phasing>0.009900</Phasing>
348 <Prephasing>0.003500</Prephasing>
353 def make_gerald_config_026(gerald_dir):
354 source = os.path.join(TESTDATA_DIR, 'gerald_config_0.2.6.xml')
355 destination = os.path.join(gerald_dir, 'config.xml')
356 shutil.copy(source, destination)
358 def make_gerald_config_100(gerald_dir):
359 source = os.path.join(TESTDATA_DIR, 'gerald_config_1.0.xml')
360 destination = os.path.join(gerald_dir, 'config.xml')
361 shutil.copy(source, destination)
363 def make_gerald_config_1_7(gerald_dir):
364 """CASAVA 1.7 gerald config"""
365 source = os.path.join(TESTDATA_DIR, 'gerald_config_1.7.xml')
366 destination = os.path.join(gerald_dir, 'config.xml')
367 shutil.copy(source, destination)
369 def make_summary_htm_100(gerald_dir):
370 source = os.path.join(TESTDATA_DIR, 'Summary-pipeline100.htm')
371 destination = os.path.join(gerald_dir, 'Summary.htm')
372 shutil.copy(source, destination)
374 def make_summary_htm_110(gerald_dir):
375 source = os.path.join(TESTDATA_DIR, 'Summary-pipeline110.htm')
376 destination = os.path.join(gerald_dir, 'Summary.htm')
377 shutil.copy(source, destination)
379 def make_summary_paired_htm(gerald_dir):
380 source = os.path.join(TESTDATA_DIR, 'Summary-paired-pipeline110.htm')
381 destination = os.path.join(gerald_dir, 'Summary.htm')
382 shutil.copy(source, destination)
384 def make_summary_ipar130_htm(gerald_dir):
385 source = os.path.join(TESTDATA_DIR, 'Summary-ipar130.htm')
386 destination = os.path.join(gerald_dir, 'Summary.htm')
387 shutil.copy(source, destination)
389 def make_summary_rta160_xml(gerald_dir):
390 source = os.path.join(TESTDATA_DIR, 'Summary-rta160.xml')
391 destination = os.path.join(gerald_dir, 'Summary.xml')
392 shutil.copy(source, destination)
395 def make_summary_casava1_7_xml(gerald_dir):
396 source = os.path.join(TESTDATA_DIR, 'Summary-casava1.7.xml')
397 destination = os.path.join(gerald_dir, 'Summary.xml')
398 shutil.copy(source, destination)
400 def make_status_rta1_12(datadir):
401 sourcedir = os.path.join(TESTDATA_DIR, '1_12')
402 status_htm = os.path.join(sourcedir, 'Status.htm')
403 destination = os.path.join(datadir, 'Status.htm')
404 shutil.copy(status_htm, destination)
406 status_dir = os.path.join(datadir, 'Status_Files')
407 status_source_dir = os.path.join(sourcedir, 'Status_Files')
408 shutil.copytree(status_source_dir, status_dir)
410 report_source_dir = os.path.join(sourcedir, 'reports')
411 report_dir = os.path.join(datadir, 'reports')
412 shutil.copytree(report_source_dir, report_dir)
414 def make_eland_results(gerald_dir):
415 eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759 ACATAGNCACAGACATAAACATAGACATAGAC U0 1 1 3 chrUextra.fa 28189829 R D.
416 >HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 chr2L.fa 8796855 R DD 24T
417 >HWI-EAS229_24_207BTAAXX:1:7:776:582 AGCTCANCCGATCGAAAACCTCNCCAAGCAAT NM 0 0 0
418 >HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 Lambda.fa 8796855 R DD 24T
421 pathname = os.path.join(gerald_dir,
422 's_%d_eland_result.txt' % (i,))
423 f = open(pathname, 'w')
424 f.write(eland_result)
427 def make_eland_multi(gerald_dir, paired=False, lane_list=LANE_LIST):
428 eland_multi = [""">HWI-EAS229_60_30DP9AAXX:1:1:1221:788 AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT NM
429 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:2 chr5.fa:55269838R0
430 >HWI-EAS229_60_30DP9AAXX:1:1:1121:379 AGAAGAGACATTAAGAGTTCCTGAAATTTATATCTGG 2:1:0 chr16.fa:46189180R1,chr7.fa:122968519R0,chr8.fa:48197174F0
431 >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
432 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:0 spike.fa/sample1:55269838R0
433 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:0 spike.fa/sample2:55269838R0
434 """, """>HWI-EAS229_60_30DP9AAXX:1:1:1221:788 AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT NM
435 >HWI-EAS229_60_30DP9AAXX:1:1:1221:788 NNNNNNNNNNNNNNGTGGTATGGCGGTGTCTGGTCGT QC
436 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:2 chr5.fa:55269838R0
437 >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
438 >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
439 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:0 spike.fa/sample1:55269838R0
440 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:0 spike.fa/sample2:55269838R0
445 pathname = os.path.join(gerald_dir,
446 's_%d_%d_eland_multi.txt' % (i,e))
447 f = open(pathname, 'w')
448 f.write(eland_multi[e-1])
452 pathname = os.path.join(gerald_dir,
453 's_%d_eland_multi.txt' % (i,))
454 f = open(pathname, 'w')
455 f.write(eland_multi[0])
458 def make_eland_export(gerald_dir, paired=False, lane_list=LANE_LIST):
459 source = os.path.join(TESTDATA_DIR, 'casava_1.7_export.txt')
462 destination = os.path.join(gerald_dir,
463 's_%d_export.txt' % (i,))
464 shutil.copy(source, destination)
467 def make_scarf(gerald_dir, lane_list=LANE_LIST):
468 seq = """HWI-EAS229_92_30VNBAAXX:1:1:0:161:NCAATTACACGACGCTAGCCCTAAAGCTATTTCGAGG:E[aaaabb^a\a_^^a[S`ba_WZUXaaaaaaUKPER
469 HWI-EAS229_92_30VNBAAXX:1:1:0:447:NAGATGCGCATTTGAAGTAGGAGCAAAAGATCAAGGT:EUabaab^baabaaaaaaaa^^Uaaaaa\aaaa__`a
470 HWI-EAS229_92_30VNBAAXX:1:1:0:1210:NATAGCCTCTATAGAAGCCACTATTATTTTTTTCTTA:EUa`]`baaaaa^XQU^a`S``S_`J_aaaaaabb^V
471 HWI-EAS229_92_30VNBAAXX:1:1:0:1867:NTGGAGCAGATATAAAAACAGATGGTGACGTTGAAGT:E[^UaaaUaba^aaa^aa^XV\baaLaLaaaaQVXV^
472 HWI-EAS229_92_30VNBAAXX:1:1:0:1898:NAGCTCGTGTCGTGAGATGTTAGGTTAAGTCCTGCAA:EK_aaaaaaaaaaaUZaaZaXM[aaaXSM\aaZ]URE
475 pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
476 f = open(pathname,'w')
480 def make_fastq(gerald_dir, lane_list=LANE_LIST):
481 seq = """@HWI-EAS229:1:2:182:712#0/1
482 AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
483 +HWI-EAS229:1:2:182:712#0/1
484 \\bab_bbaabbababbaaa]]D]bb_baabbab\baa
485 @HWI-EAS229:1:2:198:621#0/1
486 CCCCCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCCCC
487 +HWI-EAS229:1:2:198:621#0/1
488 [aaaaaaa`_`aaaaaaa[`ZDZaaaaaaaaaaaaaa
489 @HWI-EAS229:1:2:209:1321#0/1
490 AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
491 +HWI-EAS229:1:2:209:1321#0/1
492 _bbbbbaaababaabbbbab]D]aaaaaaaaaaaaaa
495 pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
496 f = open(pathname,'w')
500 UNALIGNED_READS = [1,2]
501 UNALIGNED_SAMPLES = [ (1, UNALIGNED_READS, '11111', None, None),
502 (2, UNALIGNED_READS, '11112', None, None),
503 (3, UNALIGNED_READS, '11113', 1, 'ATCACG'),
504 (3, UNALIGNED_READS, '11113', 2, 'CGATGT'),
505 (3, UNALIGNED_READS, '11113', 3, 'TTAGGC'),
506 (4, UNALIGNED_READS, '11114', 6, 'GCCAAT'),
507 (5, UNALIGNED_READS, '11115', 1, 'ATCACG'),
508 (5, UNALIGNED_READS, '11116', 7, 'ACTTGA'),
509 (5, UNALIGNED_READS, '11117', 9, 'GATCAG'),
510 (6, UNALIGNED_READS, '11118', 1, 'ATCACG'),
511 (7, UNALIGNED_READS, '11119', 2, 'CGATGT'),
512 (8, UNALIGNED_READS, '11120', 3, 'TTAGGC'),
513 (1, UNALIGNED_READS, None, None, None),
514 (2, UNALIGNED_READS, None, None, None),
515 (3, UNALIGNED_READS, None, None, None),
516 (4, UNALIGNED_READS, None, None, None),
517 (5, UNALIGNED_READS, None, None, None)]
520 def make_aligned_eland_export(aligned_dir, flowcell_id):
521 summary_source = os.path.join(TESTDATA_DIR, 'sample_summary_1_12.htm')
522 for lane, read, project_id, index_id, index_seq in UNALIGNED_SAMPLES:
523 paths = DemultiplexedPaths(aligned_dir,
529 paths.make_sample_dirs()
530 paths.make_summary_dirs()
531 summary_dest = os.path.join(paths.summary_dir, 'Sample_Summary.htm')
532 shutil.copy(summary_source, summary_dest)
534 body = get_aligned_sample_export(lane, index_seq)
535 for split in ['001','002']:
536 for read in UNALIGNED_READS:
537 suffix = 'R{0}_{1}_export.txt.gz'.format(read, split)
538 pathname = paths.make_test_filename(suffix)
539 stream = gzip.open(pathname, 'w')
544 def make_unaligned_fastqs_1_12(unaligned_dir, flowcell_id):
545 """Create a default mix of unaligned sample files
547 for lane, read, name, index_id, index in UNALIGNED_SAMPLES:
548 make_unaligned_fastq_sample_1_12(unaligned_dir,
556 def make_unaligned_fastq_sample_1_12(unaligned_dir,
564 paths = DemultiplexedPaths(unaligned_dir,
570 paths.make_sample_dirs()
572 sample_seq = get_unaligned_sample_fastq_data(flowcell_id, lane, index_seq)
573 for split in ['001','002']:
575 suffix = 'R{0}_{1}.fastq.gz'.format(read, split)
576 pathname = paths.make_test_filename(suffix)
577 stream = gzip.open(pathname, 'w')
578 stream.write(sample_seq)
581 sheetname = os.path.join(paths.sample_dir, 'SampleSheet.csv')
582 stream = open(sheetname, 'w')
583 stream.write('FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject'+os.linesep)
584 template = '{flowcell},{lane},{id},mm9,{index},Sample #{id},N,PR_indexing,Operator,{sample_project}'+os.linesep
585 stream.write(template.format(flowcell=flowcell_id,
588 index=paths.index_seq,
589 sample_project=paths.sample_project))
593 class DemultiplexedPaths(object):
594 def __init__(self, basedir, flowcell_id, lane, project_id, index_id, index_seq):
595 if lane not in LANE_LIST:
596 raise ValueError("Invalid lane ID: {0}".format(lane))
597 self.basedir = basedir
598 self.flowcell_id = flowcell_id
601 if project_id is None:
604 self.sample_id = 'lane{0}'.format(lane)
605 self.sample_project = 'Undetermined_indices'
606 self.rootname = 'lane{lane}_Undetermined_L00{lane}_'.format(
608 self.project_dir = 'Undetermined_indices'
609 self.sample_dir = 'Sample_lane{lane}'.format(lane=lane)
610 elif index_seq is None:
612 self.sample_id = project_id
613 self.sample_project = '{project_id}'.format(project_id=project_id)
614 self.rootname = '{project_id}_NoIndex_L00{lane}_'.format(
615 project_id=project_id,
617 self.project_dir = 'Project_' + self.sample_project
618 self.sample_dir = 'Sample_{project_id}'.format(
619 project_id=project_id)
621 self.index_seq = index_seq
622 self.sample_id = project_id
623 self.sample_project = '{project_id}_Index{index_id}'.format(
624 project_id=project_id,
626 self.rootname = '{project_id}_{index}_L00{lane}_'.format(
627 project_id=project_id,
630 self.project_dir = 'Project_' + self.sample_project
631 self.sample_dir = 'Sample_{project_id}'.format(
632 project_id=project_id)
634 self.project_dir = os.path.join(self.basedir, self.project_dir)
635 self.sample_dir = os.path.join(self.project_dir, self.sample_dir)
636 self.summary_dir = 'Summary_Stats_{0}'.format(self.flowcell_id)
637 self.summary_dir = os.path.join(self.project_dir, self.summary_dir)
640 def make_sample_dirs(self):
641 if not os.path.isdir(self.project_dir):
642 os.mkdir(self.project_dir)
643 if not os.path.isdir(self.sample_dir):
644 os.mkdir(self.sample_dir)
646 def make_summary_dirs(self):
647 if not os.path.isdir(self.summary_dir):
648 os.mkdir(self.summary_dir)
650 def make_test_filename(self, suffix):
651 filename = self.rootname + suffix
652 pathname = os.path.join(self.sample_dir, filename)
656 print ('index seq: {0}'.format(self.index_seq))
658 print ('project dir: {0}'.format(self.project_dir))
659 print ('sample dir: {0}'.format(self.sample_dir))
660 print ('rootname: {0}'.format(self.rootname))
661 print ('path: {0}'.format(
662 os.path.join(self.project_dir,
664 self.rootname+'R1_001.fastq.gz')))
667 def get_unaligned_sample_fastq_data(flowcell_id, lane, index_seq):
668 seq = """@HWI-ST0787:101:{flowcell}:{lane}:1101:2416:3469 1:Y:0:{index}
669 TCCTTCATTCCACCGGAGTCTGTGGAATTCTCGGGTGCCAAGGAACTCCA
671 CCCFFFFFHHHHHJJJJJJJJJIJJJJJJJJJJJJJJJJIIJJIIJJJJJ
672 @HWI-ST0787:101:{flowcell}:{lane}:1101:2677:3293 1:Y:0:{index}
673 TGGAAATCCATTGGGGTTTCCCCTGGAATTCTCGGGTGCCAAGGAACTCC
675 @CCFF3BDHHHHHIIIIIHHIIIDIIIGIIIEGIIIIIIIIIIIIIIIHH
676 @HWI-ST0787:101:{flowcell}:{lane}:1101:2616:3297 1:Y:0:{index}
677 TAATACTGCCGGGTAATGATGGCTGGAATTCTCGGGTGCCAAGGAACTCC
679 CCCFFFFFHHHHHCGHJJJJJJJJJJJJJJJJJIIJJJJJJJJJIHJJJI
680 @HWI-ST0787:101:{flowcell}:{lane}:1101:2545:3319 1:N:0:{index}
681 TCCTTCATTCCACCGGAGTCTGCTGGAATTCTCGGGTGCCAAGGAACTCC
683 CCCFFFFFHHHFHJGIGHIJHIIGHIGIGIGEHFIJJJIHIJHJIIJJIH
684 """.format(flowcell=flowcell_id, lane=lane, index=index_seq)
687 def get_aligned_sample_export(lane, index_seq):
688 body = """HWI-ST0787\t102\t{lane}\t1101\t1207\t1993\t{index}\t1\tAANGGATTCGATCCGGCTTAAGAGATGAAAACCGAAAGGGCCGACCGAA\taaBS`ccceg[`ae[dRR_[[SPPPP__ececfYYWaegh^\\ZLLY\\X`\tNM\t\t\t\t\t\t
689 HWI-ST0787\t102\t{lane}\t1101\t1478\t1997\t{index}\t1\tCAAGAACCCCGGGGGGGGGGGGGCAGAGAGGGGGAATTTTTTTTTTGTT\tBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\tNM\t\t\t\t\t\t\t\t\t\t\tN
690 HWI-ST0787\t102\t{lane}\t1101\t1625\t1994\t{index}\t1\tAANAATGCTACAGAGACAAAACAAAACTGATATGAAAGTTGAGAATAAA\tB^BS\cccgegg[Q[QQQ[`egdgffbeggfgh^^YcfgfhXaHY^O^c\tchr9.fa\t67717938\tR\t99\t72
691 HWI-ST0787\t102\t{lane}\t1101\t1625\t1994\t{index}\t1\tAANAATGCTACAGAGACAAAACAAAACTGATATGAAAGTTGAGAATAAA\tB^BS\cccgegg[Q[QQQ[`egdgffbeggfgh^^YcfgfhXaHY^O^c\t3:4:3\t\t\t\t\t\t\t\t\t\t\tY
692 """.format(lane=lane, index=index_seq)
695 def print_ls_tree(root):
696 """List tree contents, useful for debugging.
698 for dirpath, dirnames, filenames in os.walk(root):
699 for filename in filenames:
700 print os.path.join(dirpath, filename)
703 class BaseCallInfo(object):
704 """Provide customization for how to setup the base call mock data
706 def __init__(self, qseq_file, tile_list, basecall_summary):
707 self.qseq_file = qseq_file
708 self.tile_list = tile_list
709 self.basecall_summary = basecall_summary
711 # First generation HiSeq Flowcell
712 ABXX_BASE_CALL_INFO = BaseCallInfo(
713 qseq_file='AA01CCABXX_8_2_2207_qseq.txt',
714 tile_list = HISEQ_TILE_LIST,
715 basecall_summary = 'AA01CCABXX_BustardSummary.xml')