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_rta_intensities_1460(data_dir, version='1.4.6.0'):
106 Construct an artificial RTA Intensities parameter file and directory
108 intensities_dir = os.path.join(data_dir, 'Intensities')
109 if not os.path.exists(intensities_dir):
110 os.mkdir(intensities_dir)
112 param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config.xml')
113 shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
115 return intensities_dir
117 def make_rta_basecalls_1460(intensities_dir):
119 Construct an artificial RTA Intensities parameter file and directory
121 basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
122 if not os.path.exists(basecalls_dir):
123 os.mkdir(basecalls_dir)
125 param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config.xml')
126 shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
130 def make_rta_intensities_1870(data_dir, version='1.8.70.0'):
132 Construct an artificial RTA Intensities parameter file and directory
134 intensities_dir = os.path.join(data_dir, 'Intensities')
135 if not os.path.exists(intensities_dir):
136 os.mkdir(intensities_dir)
138 param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config_1870.xml')
139 shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
141 return intensities_dir
143 def make_rta_intensities_1_10(data_dir, version='1.10.36.0'):
145 Construct an artificial RTA Intensities parameter file and directory
147 intensities_dir = os.path.join(data_dir, 'Intensities')
148 if not os.path.exists(intensities_dir):
149 os.mkdir(intensities_dir)
151 param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config_1.10.xml')
152 shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
154 return intensities_dir
156 def make_rta_intensities_1_12(data_dir, version='1.12.4.2'):
158 Construct an artificial RTA Intensities parameter file and directory
160 intensities_dir = os.path.join(data_dir, 'Intensities')
161 if not os.path.exists(intensities_dir):
162 os.mkdir(intensities_dir)
164 param_file = os.path.join(TESTDATA_DIR, '1_12',
165 'rta_intensities_config_1.12.4.2.xml')
166 shutil.copy(param_file, os.path.join(intensities_dir, 'RTAConfig.xml'))
168 return intensities_dir
170 def make_rta_basecalls_1870(intensities_dir):
172 Construct an artificial RTA Intensities parameter file and directory
174 basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
175 if not os.path.exists(basecalls_dir):
176 os.mkdir(basecalls_dir)
178 param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config_1870.xml')
179 shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
183 def make_rta_basecalls_1_10(intensities_dir):
185 Construct an artificial RTA Intensities parameter file and directory
187 basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
188 if not os.path.exists(basecalls_dir):
189 os.mkdir(basecalls_dir)
191 make_qseqs(basecalls_dir, basecall_info=ABXX_BASE_CALL_INFO)
192 param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config_1.10.xml')
193 shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
197 def make_rta_basecalls_1_12(intensities_dir):
199 Construct an artificial RTA Intensities parameter file and directory
201 basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
202 if not os.path.exists(basecalls_dir):
203 os.mkdir(basecalls_dir)
205 make_qseqs(basecalls_dir, basecall_info=ABXX_BASE_CALL_INFO)
206 param_file = os.path.join(TESTDATA_DIR, '1_12',
207 'rta_basecalls_config_1.12.4.2.xml')
208 shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
213 def make_qseqs(bustard_dir, basecall_info=None):
215 Fill gerald directory with qseq files
217 if basecall_info is None:
218 qseq_file = '42BRJAAXX_8_1_0039_qseq.txt'
219 tile_list = TILE_LIST
220 summary_file = '42BRJAAXX_BustardSummary.xml'
222 qseq_file = basecall_info.qseq_file
223 tile_list = basecall_info.tile_list
224 summary_file = basecall_info.basecall_summary
226 # 42BRJ 8 1 0039 happened to be a better than usual tile, in that there
227 # was actually sequence at the start
228 source = os.path.join(TESTDATA_DIR, qseq_file)
229 destdir = bustard_dir
230 if not os.path.isdir(destdir):
233 for lane in LANE_LIST:
234 for tile in tile_list:
235 destination = os.path.join(bustard_dir, 's_%d_1_%04d_qseq.txt' % (lane, tile))
236 shutil.copy(source, destination)
238 make_matrix_dir(bustard_dir)
239 make_phasing_dir(bustard_dir)
241 summary_source = os.path.join(TESTDATA_DIR, summary_file)
242 summary_dest = os.path.join(bustard_dir, 'BustardSummary.xml')
243 shutil.copy(summary_source, summary_dest)
247 def make_scores(gerald_dir, in_temp=True):
249 Fill gerald directory with score temp files
250 will create the directory if it doesn't exist.
252 source = os.path.join(TESTDATA_DIR, 's_1_0001_score.txt')
255 destdir = os.path.join(destdir, 'Temp')
256 if not os.path.isdir(destdir):
259 for lane in LANE_LIST:
260 for tile in TILE_LIST:
261 destination = os.path.join(destdir, 's_%d_%04d_score.txt' % (lane, tile))
262 shutil.copy(source, destination)
266 def make_matrix_dir(bustard_dir):
268 Create several matrix files in <bustard_dir>/Matrix/
272 destdir = os.path.join(bustard_dir, 'Matrix')
273 if not os.path.isdir(destdir):
276 source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_02_matrix.txt')
277 for lane in LANE_LIST:
278 destination = os.path.join(destdir, 's_%d_02_matrix.txt' % ( lane, ))
279 shutil.copy(source, destination)
281 def make_matrix(matrix_filename):
282 contents = """# Auto-generated frequency response matrix
287 0.77 0.15 -0.04 -0.04
288 0.76 1.02 -0.05 -0.06
289 -0.10 -0.10 1.17 -0.03
290 -0.13 -0.12 0.80 1.27
292 f = open(matrix_filename, 'w')
296 def make_matrix_dir_rta160(bustard_dir):
298 Create several matrix files in <bustard_dir>/Matrix/
300 destdir = os.path.join(bustard_dir, 'Matrix')
301 if not os.path.isdir(destdir):
304 source = os.path.join(TESTDATA_DIR, '61MMFAAXX_4_1_matrix.txt')
305 lane_fragments = [ "_%d" % (l,) for l in LANE_LIST]
306 for fragment in lane_fragments:
307 destination = os.path.join(destdir, 's%s_1_matrix.txt' % ( fragment, ))
308 shutil.copy(source, destination)
310 def make_matrix_dir_rta_1_10(bustard_dir):
311 make_matrix_dir_rta160(bustard_dir)
313 def make_matrix_dir_rta_1_12(bustard_dir):
314 make_matrix_dir_rta160(bustard_dir)
316 def make_phasing_dir(bustard_dir):
318 Create several phasing files in <bustard_dir>/Phasing/
322 destdir = os.path.join(bustard_dir, 'Phasing')
323 if not os.path.isdir(destdir):
326 source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_01_phasing.xml')
327 for lane in LANE_LIST:
328 destination = os.path.join(destdir, 's_%d_01_phasing.xml' % ( lane, ))
329 shutil.copy(source, destination)
331 def make_phasing_params(bustard_dir):
332 for lane in LANE_LIST:
333 pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
334 f = open(pathname, 'w')
335 f.write("""<Parameters>
336 <Phasing>0.009900</Phasing>
337 <Prephasing>0.003500</Prephasing>
342 def make_gerald_config_026(gerald_dir):
343 source = os.path.join(TESTDATA_DIR, 'gerald_config_0.2.6.xml')
344 destination = os.path.join(gerald_dir, 'config.xml')
345 shutil.copy(source, destination)
347 def make_gerald_config_100(gerald_dir):
348 source = os.path.join(TESTDATA_DIR, 'gerald_config_1.0.xml')
349 destination = os.path.join(gerald_dir, 'config.xml')
350 shutil.copy(source, destination)
352 def make_gerald_config_1_7(gerald_dir):
353 """CASAVA 1.7 gerald config"""
354 source = os.path.join(TESTDATA_DIR, 'gerald_config_1.7.xml')
355 destination = os.path.join(gerald_dir, 'config.xml')
356 shutil.copy(source, destination)
358 def make_summary_htm_100(gerald_dir):
359 source = os.path.join(TESTDATA_DIR, 'Summary-pipeline100.htm')
360 destination = os.path.join(gerald_dir, 'Summary.htm')
361 shutil.copy(source, destination)
363 def make_summary_htm_110(gerald_dir):
364 source = os.path.join(TESTDATA_DIR, 'Summary-pipeline110.htm')
365 destination = os.path.join(gerald_dir, 'Summary.htm')
366 shutil.copy(source, destination)
368 def make_summary_paired_htm(gerald_dir):
369 source = os.path.join(TESTDATA_DIR, 'Summary-paired-pipeline110.htm')
370 destination = os.path.join(gerald_dir, 'Summary.htm')
371 shutil.copy(source, destination)
373 def make_summary_ipar130_htm(gerald_dir):
374 source = os.path.join(TESTDATA_DIR, 'Summary-ipar130.htm')
375 destination = os.path.join(gerald_dir, 'Summary.htm')
376 shutil.copy(source, destination)
378 def make_summary_rta160_xml(gerald_dir):
379 source = os.path.join(TESTDATA_DIR, 'Summary-rta160.xml')
380 destination = os.path.join(gerald_dir, 'Summary.xml')
381 shutil.copy(source, destination)
384 def make_summary_casava1_7_xml(gerald_dir):
385 source = os.path.join(TESTDATA_DIR, 'Summary-casava1.7.xml')
386 destination = os.path.join(gerald_dir, 'Summary.xml')
387 shutil.copy(source, destination)
389 def make_status_rta1_12(datadir):
390 sourcedir = os.path.join(TESTDATA_DIR, '1_12')
391 status_htm = os.path.join(sourcedir, 'Status.htm')
392 destination = os.path.join(datadir, 'Status.htm')
393 shutil.copy(status_htm, destination)
395 status_dir = os.path.join(datadir, 'Status_Files')
396 status_source_dir = os.path.join(sourcedir, 'Status_Files')
397 shutil.copytree(status_source_dir, status_dir)
399 report_source_dir = os.path.join(sourcedir, 'reports')
400 report_dir = os.path.join(datadir, 'reports')
401 shutil.copytree(report_source_dir, report_dir)
403 def make_eland_results(gerald_dir):
404 eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759 ACATAGNCACAGACATAAACATAGACATAGAC U0 1 1 3 chrUextra.fa 28189829 R D.
405 >HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 chr2L.fa 8796855 R DD 24T
406 >HWI-EAS229_24_207BTAAXX:1:7:776:582 AGCTCANCCGATCGAAAACCTCNCCAAGCAAT NM 0 0 0
407 >HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 Lambda.fa 8796855 R DD 24T
410 pathname = os.path.join(gerald_dir,
411 's_%d_eland_result.txt' % (i,))
412 f = open(pathname, 'w')
413 f.write(eland_result)
416 def make_eland_multi(gerald_dir, paired=False, lane_list=LANE_LIST):
417 eland_multi = [""">HWI-EAS229_60_30DP9AAXX:1:1:1221:788 AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT NM
418 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:2 chr5.fa:55269838R0
419 >HWI-EAS229_60_30DP9AAXX:1:1:1121:379 AGAAGAGACATTAAGAGTTCCTGAAATTTATATCTGG 2:1:0 chr16.fa:46189180R1,chr7.fa:122968519R0,chr8.fa:48197174F0
420 >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
421 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:0 spike.fa/sample1:55269838R0
422 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:0 spike.fa/sample2:55269838R0
423 """, """>HWI-EAS229_60_30DP9AAXX:1:1:1221:788 AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT NM
424 >HWI-EAS229_60_30DP9AAXX:1:1:1221:788 NNNNNNNNNNNNNNGTGGTATGGCGGTGTCTGGTCGT QC
425 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:2 chr5.fa:55269838R0
426 >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
427 >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
428 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:0 spike.fa/sample1:55269838R0
429 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:0 spike.fa/sample2:55269838R0
434 pathname = os.path.join(gerald_dir,
435 's_%d_%d_eland_multi.txt' % (i,e))
436 f = open(pathname, 'w')
437 f.write(eland_multi[e-1])
441 pathname = os.path.join(gerald_dir,
442 's_%d_eland_multi.txt' % (i,))
443 f = open(pathname, 'w')
444 f.write(eland_multi[0])
447 def make_eland_export(gerald_dir, paired=False, lane_list=LANE_LIST):
448 source = os.path.join(TESTDATA_DIR, 'casava_1.7_export.txt')
451 destination = os.path.join(gerald_dir,
452 's_%d_export.txt' % (i,))
453 shutil.copy(source, destination)
456 def make_scarf(gerald_dir, lane_list=LANE_LIST):
457 seq = """HWI-EAS229_92_30VNBAAXX:1:1:0:161:NCAATTACACGACGCTAGCCCTAAAGCTATTTCGAGG:E[aaaabb^a\a_^^a[S`ba_WZUXaaaaaaUKPER
458 HWI-EAS229_92_30VNBAAXX:1:1:0:447:NAGATGCGCATTTGAAGTAGGAGCAAAAGATCAAGGT:EUabaab^baabaaaaaaaa^^Uaaaaa\aaaa__`a
459 HWI-EAS229_92_30VNBAAXX:1:1:0:1210:NATAGCCTCTATAGAAGCCACTATTATTTTTTTCTTA:EUa`]`baaaaa^XQU^a`S``S_`J_aaaaaabb^V
460 HWI-EAS229_92_30VNBAAXX:1:1:0:1867:NTGGAGCAGATATAAAAACAGATGGTGACGTTGAAGT:E[^UaaaUaba^aaa^aa^XV\baaLaLaaaaQVXV^
461 HWI-EAS229_92_30VNBAAXX:1:1:0:1898:NAGCTCGTGTCGTGAGATGTTAGGTTAAGTCCTGCAA:EK_aaaaaaaaaaaUZaaZaXM[aaaXSM\aaZ]URE
464 pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
465 f = open(pathname,'w')
469 def make_fastq(gerald_dir, lane_list=LANE_LIST):
470 seq = """@HWI-EAS229:1:2:182:712#0/1
471 AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
472 +HWI-EAS229:1:2:182:712#0/1
473 \\bab_bbaabbababbaaa]]D]bb_baabbab\baa
474 @HWI-EAS229:1:2:198:621#0/1
475 CCCCCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCCCC
476 +HWI-EAS229:1:2:198:621#0/1
477 [aaaaaaa`_`aaaaaaa[`ZDZaaaaaaaaaaaaaa
478 @HWI-EAS229:1:2:209:1321#0/1
479 AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
480 +HWI-EAS229:1:2:209:1321#0/1
481 _bbbbbaaababaabbbbab]D]aaaaaaaaaaaaaa
484 pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
485 f = open(pathname,'w')
489 UNALIGNED_READS = [1,2]
490 UNALIGNED_SAMPLES = [ (1, UNALIGNED_READS, '11111', None, None),
491 (2, UNALIGNED_READS, '11112', None, None),
492 (3, UNALIGNED_READS, '11113', 1, 'ATCACG'),
493 (3, UNALIGNED_READS, '11113', 2, 'CGATGT'),
494 (3, UNALIGNED_READS, '11113', 3, 'TTAGGC'),
495 (4, UNALIGNED_READS, '11114', 6, 'GCCAAT'),
496 (5, UNALIGNED_READS, '11115', 1, 'ATCACG'),
497 (5, UNALIGNED_READS, '11116', 7, 'ACTTGA'),
498 (5, UNALIGNED_READS, '11117', 9, 'GATCAG'),
499 (6, UNALIGNED_READS, '11118', 1, 'ATCACG'),
500 (7, UNALIGNED_READS, '11119', 2, 'CGATGT'),
501 (8, UNALIGNED_READS, '11120', 3, 'TTAGGC'),
502 (1, UNALIGNED_READS, None, None, None),
503 (2, UNALIGNED_READS, None, None, None),
504 (3, UNALIGNED_READS, None, None, None),
505 (4, UNALIGNED_READS, None, None, None),
506 (5, UNALIGNED_READS, None, None, None)]
509 def make_aligned_eland_export(aligned_dir, flowcell_id):
510 summary_source = os.path.join(TESTDATA_DIR, 'sample_summary_1_12.htm')
511 for lane, read, project_id, index_id, index_seq in UNALIGNED_SAMPLES:
512 paths = DemultiplexedPaths(aligned_dir,
518 paths.make_sample_dirs()
519 paths.make_summary_dirs()
520 summary_dest = os.path.join(paths.summary_dir, 'Sample_Summary.htm')
521 shutil.copy(summary_source, summary_dest)
523 body = get_aligned_sample_export(lane, index_seq)
524 for split in ['001','002']:
525 for read in UNALIGNED_READS:
526 suffix = 'R{0}_{1}_export.txt.gz'.format(read, split)
527 pathname = paths.make_test_filename(suffix)
528 stream = gzip.open(pathname, 'w')
533 def make_unaligned_fastqs_1_12(unaligned_dir, flowcell_id):
534 """Create a default mix of unaligned sample files
536 for lane, read, name, index_id, index in UNALIGNED_SAMPLES:
537 make_unaligned_fastq_sample_1_12(unaligned_dir,
545 def make_unaligned_fastq_sample_1_12(unaligned_dir,
553 paths = DemultiplexedPaths(unaligned_dir,
559 paths.make_sample_dirs()
561 sample_seq = get_unaligned_sample_fastq_data(flowcell_id, lane, index_seq)
562 for split in ['001','002']:
564 suffix = 'R{0}_{1}.fastq.gz'.format(read, split)
565 pathname = paths.make_test_filename(suffix)
566 stream = gzip.open(pathname, 'w')
567 stream.write(sample_seq)
570 sheetname = os.path.join(paths.sample_dir, 'SampleSheet.csv')
571 stream = open(sheetname, 'w')
572 stream.write('FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject'+os.linesep)
573 template = '{flowcell},{lane},{id},mm9,{index},Sample #{id},N,PR_indexing,Operator,{sample_project}'+os.linesep
574 stream.write(template.format(flowcell=flowcell_id,
577 index=paths.index_seq,
578 sample_project=paths.sample_project))
582 class DemultiplexedPaths(object):
583 def __init__(self, basedir, flowcell_id, lane, project_id, index_id, index_seq):
584 if lane not in LANE_LIST:
585 raise ValueError("Invalid lane ID: {0}".format(lane))
586 self.basedir = basedir
587 self.flowcell_id = flowcell_id
590 if project_id is None:
593 self.sample_id = 'lane{0}'.format(lane)
594 self.sample_project = 'Undetermined_indices'
595 self.rootname = 'lane{lane}_Undetermined_L00{lane}_'.format(
597 self.project_dir = 'Undetermined_indices'
598 self.sample_dir = 'Sample_lane{lane}'.format(lane=lane)
599 elif index_seq is None:
601 self.sample_id = project_id
602 self.sample_project = '{project_id}'.format(project_id=project_id)
603 self.rootname = '{project_id}_NoIndex_L00{lane}_'.format(
604 project_id=project_id,
606 self.project_dir = 'Project_' + self.sample_project
607 self.sample_dir = 'Sample_{project_id}'.format(
608 project_id=project_id)
610 self.index_seq = index_seq
611 self.sample_id = project_id
612 self.sample_project = '{project_id}_Index{index_id}'.format(
613 project_id=project_id,
615 self.rootname = '{project_id}_{index}_L00{lane}_'.format(
616 project_id=project_id,
619 self.project_dir = 'Project_' + self.sample_project
620 self.sample_dir = 'Sample_{project_id}'.format(
621 project_id=project_id)
623 self.project_dir = os.path.join(self.basedir, self.project_dir)
624 self.sample_dir = os.path.join(self.project_dir, self.sample_dir)
625 self.summary_dir = 'Summary_Stats_{0}'.format(self.flowcell_id)
626 self.summary_dir = os.path.join(self.project_dir, self.summary_dir)
629 def make_sample_dirs(self):
630 if not os.path.isdir(self.project_dir):
631 os.mkdir(self.project_dir)
632 if not os.path.isdir(self.sample_dir):
633 os.mkdir(self.sample_dir)
635 def make_summary_dirs(self):
636 if not os.path.isdir(self.summary_dir):
637 os.mkdir(self.summary_dir)
639 def make_test_filename(self, suffix):
640 filename = self.rootname + suffix
641 pathname = os.path.join(self.sample_dir, filename)
645 print ('index seq: {0}'.format(self.index_seq))
647 print ('project dir: {0}'.format(self.project_dir))
648 print ('sample dir: {0}'.format(self.sample_dir))
649 print ('rootname: {0}'.format(self.rootname))
650 print ('path: {0}'.format(
651 os.path.join(self.project_dir,
653 self.rootname+'R1_001.fastq.gz')))
656 def get_unaligned_sample_fastq_data(flowcell_id, lane, index_seq):
657 seq = """@HWI-ST0787:101:{flowcell}:{lane}:1101:2416:3469 1:Y:0:{index}
658 TCCTTCATTCCACCGGAGTCTGTGGAATTCTCGGGTGCCAAGGAACTCCA
660 CCCFFFFFHHHHHJJJJJJJJJIJJJJJJJJJJJJJJJJIIJJIIJJJJJ
661 @HWI-ST0787:101:{flowcell}:{lane}:1101:2677:3293 1:Y:0:{index}
662 TGGAAATCCATTGGGGTTTCCCCTGGAATTCTCGGGTGCCAAGGAACTCC
664 @CCFF3BDHHHHHIIIIIHHIIIDIIIGIIIEGIIIIIIIIIIIIIIIHH
665 @HWI-ST0787:101:{flowcell}:{lane}:1101:2616:3297 1:Y:0:{index}
666 TAATACTGCCGGGTAATGATGGCTGGAATTCTCGGGTGCCAAGGAACTCC
668 CCCFFFFFHHHHHCGHJJJJJJJJJJJJJJJJJIIJJJJJJJJJIHJJJI
669 @HWI-ST0787:101:{flowcell}:{lane}:1101:2545:3319 1:N:0:{index}
670 TCCTTCATTCCACCGGAGTCTGCTGGAATTCTCGGGTGCCAAGGAACTCC
672 CCCFFFFFHHHFHJGIGHIJHIIGHIGIGIGEHFIJJJIHIJHJIIJJIH
673 """.format(flowcell=flowcell_id, lane=lane, index=index_seq)
676 def get_aligned_sample_export(lane, index_seq):
677 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
678 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
679 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
680 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
681 """.format(lane=lane, index=index_seq)
684 def print_ls_tree(root):
685 """List tree contents, useful for debugging.
687 for dirpath, dirnames, filenames in os.walk(root):
688 for filename in filenames:
689 print os.path.join(dirpath, filename)
692 class BaseCallInfo(object):
693 """Provide customization for how to setup the base call mock data
695 def __init__(self, qseq_file, tile_list, basecall_summary):
696 self.qseq_file = qseq_file
697 self.tile_list = tile_list
698 self.basecall_summary = basecall_summary
700 # First generation HiSeq Flowcell
701 ABXX_BASE_CALL_INFO = BaseCallInfo(
702 qseq_file='AA01CCABXX_8_2_2207_qseq.txt',
703 tile_list = HISEQ_TILE_LIST,
704 basecall_summary = 'AA01CCABXX_BustardSummary.xml')