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_bustard_config132(image_dir):
54 source = os.path.join(TESTDATA_DIR, 'bustard-config132.xml')
55 destination = os.path.join(image_dir, 'config.xml')
56 shutil.copy(source, destination)
58 def make_aligned_config_1_12(aligned_dir):
59 """This is rouglhly equivalent to the old gerald file"""
60 source = os.path.join(TESTDATA_DIR, '1_12', 'aligned_config_1_12.xml')
61 destination = os.path.join(aligned_dir, 'config.xml')
62 shutil.copy(source, destination)
64 def make_unaligned_config_1_12(unaligned_dir):
65 demultiplex_pairs = [ # (src,
67 (os.path.join(TESTDATA_DIR, '1_12', 'demultiplex_1.12.4.2.xml'),
68 os.path.join(unaligned_dir, 'DemultiplexConfig.xml')),
69 (os.path.join(TESTDATA_DIR, '1_12',
70 'demultiplexed_bustard_1.12.4.2.xml'),
71 os.path.join(unaligned_dir, 'DemultiplexedBustardConfig.xml')),
72 (os.path.join(TESTDATA_DIR, '1_12',
73 'demultiplexed_summary_1.12.4.2.xml'),
74 os.path.join(unaligned_dir, 'DemultiplexedBustardSummary.xml')),
76 for src, dest in demultiplex_pairs:
77 shutil.copy(src, dest)
79 def make_rta_intensities_1460(data_dir, version='1.4.6.0'):
81 Construct an artificial RTA Intensities parameter file and directory
83 intensities_dir = os.path.join(data_dir, 'Intensities')
84 if not os.path.exists(intensities_dir):
85 os.mkdir(intensities_dir)
87 param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config.xml')
88 shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
90 return intensities_dir
92 def make_rta_basecalls_1460(intensities_dir):
94 Construct an artificial RTA Intensities parameter file and directory
96 basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
97 if not os.path.exists(basecalls_dir):
98 os.mkdir(basecalls_dir)
100 param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config.xml')
101 shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
105 def make_rta_intensities_1870(data_dir, version='1.8.70.0'):
107 Construct an artificial RTA Intensities parameter file and directory
109 intensities_dir = os.path.join(data_dir, 'Intensities')
110 if not os.path.exists(intensities_dir):
111 os.mkdir(intensities_dir)
113 param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config_1870.xml')
114 shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
116 return intensities_dir
118 def make_rta_intensities_1_10(data_dir, version='1.10.36.0'):
120 Construct an artificial RTA Intensities parameter file and directory
122 intensities_dir = os.path.join(data_dir, 'Intensities')
123 if not os.path.exists(intensities_dir):
124 os.mkdir(intensities_dir)
126 param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config_1.10.xml')
127 shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
129 return intensities_dir
131 def make_rta_intensities_1_12(data_dir, version='1.12.4.2'):
133 Construct an artificial RTA Intensities parameter file and directory
135 intensities_dir = os.path.join(data_dir, 'Intensities')
136 if not os.path.exists(intensities_dir):
137 os.mkdir(intensities_dir)
139 param_file = os.path.join(TESTDATA_DIR, '1_12',
140 'rta_intensities_config_1.12.4.2.xml')
141 shutil.copy(param_file, os.path.join(intensities_dir, 'RTAConfig.xml'))
143 return intensities_dir
145 def make_rta_basecalls_1870(intensities_dir):
147 Construct an artificial RTA Intensities parameter file and directory
149 basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
150 if not os.path.exists(basecalls_dir):
151 os.mkdir(basecalls_dir)
153 param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config_1870.xml')
154 shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
158 def make_rta_basecalls_1_10(intensities_dir):
160 Construct an artificial RTA Intensities parameter file and directory
162 basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
163 if not os.path.exists(basecalls_dir):
164 os.mkdir(basecalls_dir)
166 make_qseqs(basecalls_dir, basecall_info=ABXX_BASE_CALL_INFO)
167 param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config_1.10.xml')
168 shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
172 def make_rta_basecalls_1_12(intensities_dir):
174 Construct an artificial RTA Intensities parameter file and directory
176 basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
177 if not os.path.exists(basecalls_dir):
178 os.mkdir(basecalls_dir)
180 make_qseqs(basecalls_dir, basecall_info=ABXX_BASE_CALL_INFO)
181 param_file = os.path.join(TESTDATA_DIR, '1_12',
182 'rta_basecalls_config_1.12.4.2.xml')
183 shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
188 def make_qseqs(bustard_dir, basecall_info=None):
190 Fill gerald directory with qseq files
192 if basecall_info is None:
193 qseq_file = '42BRJAAXX_8_1_0039_qseq.txt'
194 tile_list = TILE_LIST
195 summary_file = '42BRJAAXX_BustardSummary.xml'
197 qseq_file = basecall_info.qseq_file
198 tile_list = basecall_info.tile_list
199 summary_file = basecall_info.basecall_summary
201 # 42BRJ 8 1 0039 happened to be a better than usual tile, in that there
202 # was actually sequence at the start
203 source = os.path.join(TESTDATA_DIR, qseq_file)
204 destdir = bustard_dir
205 if not os.path.isdir(destdir):
208 for lane in LANE_LIST:
209 for tile in tile_list:
210 destination = os.path.join(bustard_dir, 's_%d_1_%04d_qseq.txt' % (lane, tile))
211 shutil.copy(source, destination)
213 make_matrix_dir(bustard_dir)
214 make_phasing_dir(bustard_dir)
216 summary_source = os.path.join(TESTDATA_DIR, summary_file)
217 summary_dest = os.path.join(bustard_dir, 'BustardSummary.xml')
218 shutil.copy(summary_source, summary_dest)
222 def make_scores(gerald_dir, in_temp=True):
224 Fill gerald directory with score temp files
225 will create the directory if it doesn't exist.
227 source = os.path.join(TESTDATA_DIR, 's_1_0001_score.txt')
230 destdir = os.path.join(destdir, 'Temp')
231 if not os.path.isdir(destdir):
234 for lane in LANE_LIST:
235 for tile in TILE_LIST:
236 destination = os.path.join(destdir, 's_%d_%04d_score.txt' % (lane, tile))
237 shutil.copy(source, destination)
241 def make_matrix_dir(bustard_dir):
243 Create several matrix files in <bustard_dir>/Matrix/
247 destdir = os.path.join(bustard_dir, 'Matrix')
248 if not os.path.isdir(destdir):
251 source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_02_matrix.txt')
252 for lane in LANE_LIST:
253 destination = os.path.join(destdir, 's_%d_02_matrix.txt' % ( lane, ))
254 shutil.copy(source, destination)
256 def make_matrix(matrix_filename):
257 contents = """# Auto-generated frequency response matrix
262 0.77 0.15 -0.04 -0.04
263 0.76 1.02 -0.05 -0.06
264 -0.10 -0.10 1.17 -0.03
265 -0.13 -0.12 0.80 1.27
267 f = open(matrix_filename, 'w')
271 def make_matrix_dir_rta160(bustard_dir):
273 Create several matrix files in <bustard_dir>/Matrix/
275 destdir = os.path.join(bustard_dir, 'Matrix')
276 if not os.path.isdir(destdir):
279 source = os.path.join(TESTDATA_DIR, '61MMFAAXX_4_1_matrix.txt')
280 lane_fragments = [ "_%d" % (l,) for l in LANE_LIST]
281 for fragment in lane_fragments:
282 destination = os.path.join(destdir, 's%s_1_matrix.txt' % ( fragment, ))
283 shutil.copy(source, destination)
285 def make_matrix_dir_rta_1_10(bustard_dir):
286 make_matrix_dir_rta160(bustard_dir)
288 def make_matrix_dir_rta_1_12(bustard_dir):
289 make_matrix_dir_rta160(bustard_dir)
291 def make_phasing_dir(bustard_dir):
293 Create several phasing files in <bustard_dir>/Phasing/
297 destdir = os.path.join(bustard_dir, 'Phasing')
298 if not os.path.isdir(destdir):
301 source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_01_phasing.xml')
302 for lane in LANE_LIST:
303 destination = os.path.join(destdir, 's_%d_01_phasing.xml' % ( lane, ))
304 shutil.copy(source, destination)
306 def make_phasing_params(bustard_dir):
307 for lane in LANE_LIST:
308 pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
309 f = open(pathname, 'w')
310 f.write("""<Parameters>
311 <Phasing>0.009900</Phasing>
312 <Prephasing>0.003500</Prephasing>
317 def make_gerald_config_026(gerald_dir):
318 source = os.path.join(TESTDATA_DIR, 'gerald_config_0.2.6.xml')
319 destination = os.path.join(gerald_dir, 'config.xml')
320 shutil.copy(source, destination)
322 def make_gerald_config_100(gerald_dir):
323 source = os.path.join(TESTDATA_DIR, 'gerald_config_1.0.xml')
324 destination = os.path.join(gerald_dir, 'config.xml')
325 shutil.copy(source, destination)
327 def make_gerald_config_1_7(gerald_dir):
328 """CASAVA 1.7 gerald config"""
329 source = os.path.join(TESTDATA_DIR, 'gerald_config_1.7.xml')
330 destination = os.path.join(gerald_dir, 'config.xml')
331 shutil.copy(source, destination)
333 def make_summary_htm_100(gerald_dir):
334 source = os.path.join(TESTDATA_DIR, 'Summary-pipeline100.htm')
335 destination = os.path.join(gerald_dir, 'Summary.htm')
336 shutil.copy(source, destination)
338 def make_summary_htm_110(gerald_dir):
339 source = os.path.join(TESTDATA_DIR, 'Summary-pipeline110.htm')
340 destination = os.path.join(gerald_dir, 'Summary.htm')
341 shutil.copy(source, destination)
343 def make_summary_paired_htm(gerald_dir):
344 source = os.path.join(TESTDATA_DIR, 'Summary-paired-pipeline110.htm')
345 destination = os.path.join(gerald_dir, 'Summary.htm')
346 shutil.copy(source, destination)
348 def make_summary_ipar130_htm(gerald_dir):
349 source = os.path.join(TESTDATA_DIR, 'Summary-ipar130.htm')
350 destination = os.path.join(gerald_dir, 'Summary.htm')
351 shutil.copy(source, destination)
353 def make_summary_rta160_xml(gerald_dir):
354 source = os.path.join(TESTDATA_DIR, 'Summary-rta160.xml')
355 destination = os.path.join(gerald_dir, 'Summary.xml')
356 shutil.copy(source, destination)
359 def make_summary_casava1_7_xml(gerald_dir):
360 source = os.path.join(TESTDATA_DIR, 'Summary-casava1.7.xml')
361 destination = os.path.join(gerald_dir, 'Summary.xml')
362 shutil.copy(source, destination)
364 def make_status_rta1_12(datadir):
365 sourcedir = os.path.join(TESTDATA_DIR, '1_12')
366 status_htm = os.path.join(sourcedir, 'Status.htm')
367 destination = os.path.join(datadir, 'Status.htm')
368 shutil.copy(status_htm, destination)
370 status_dir = os.path.join(datadir, 'Status_Files')
371 status_source_dir = os.path.join(sourcedir, 'Status_Files')
372 shutil.copytree(status_source_dir, status_dir)
374 report_source_dir = os.path.join(sourcedir, 'reports')
375 report_dir = os.path.join(datadir, 'reports')
376 shutil.copytree(report_source_dir, report_dir)
378 def make_eland_results(gerald_dir):
379 eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759 ACATAGNCACAGACATAAACATAGACATAGAC U0 1 1 3 chrUextra.fa 28189829 R D.
380 >HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 chr2L.fa 8796855 R DD 24T
381 >HWI-EAS229_24_207BTAAXX:1:7:776:582 AGCTCANCCGATCGAAAACCTCNCCAAGCAAT NM 0 0 0
382 >HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 Lambda.fa 8796855 R DD 24T
385 pathname = os.path.join(gerald_dir,
386 's_%d_eland_result.txt' % (i,))
387 f = open(pathname, 'w')
388 f.write(eland_result)
391 def make_eland_multi(gerald_dir, paired=False, lane_list=LANE_LIST):
392 eland_multi = [""">HWI-EAS229_60_30DP9AAXX:1:1:1221:788 AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT NM
393 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:2 chr5.fa:55269838R0
394 >HWI-EAS229_60_30DP9AAXX:1:1:1121:379 AGAAGAGACATTAAGAGTTCCTGAAATTTATATCTGG 2:1:0 chr16.fa:46189180R1,chr7.fa:122968519R0,chr8.fa:48197174F0
395 >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
396 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:0 spike.fa/sample1:55269838R0
397 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:0 spike.fa/sample2:55269838R0
398 """, """>HWI-EAS229_60_30DP9AAXX:1:1:1221:788 AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT NM
399 >HWI-EAS229_60_30DP9AAXX:1:1:1221:788 NNNNNNNNNNNNNNGTGGTATGGCGGTGTCTGGTCGT QC
400 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:2 chr5.fa:55269838R0
401 >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
402 >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
403 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:0 spike.fa/sample1:55269838R0
404 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:0 spike.fa/sample2:55269838R0
409 pathname = os.path.join(gerald_dir,
410 's_%d_%d_eland_multi.txt' % (i,e))
411 f = open(pathname, 'w')
412 f.write(eland_multi[e-1])
416 pathname = os.path.join(gerald_dir,
417 's_%d_eland_multi.txt' % (i,))
418 f = open(pathname, 'w')
419 f.write(eland_multi[0])
422 def make_eland_export(gerald_dir, paired=False, lane_list=LANE_LIST):
423 source = os.path.join(TESTDATA_DIR, 'casava_1.7_export.txt')
426 destination = os.path.join(gerald_dir,
427 's_%d_export.txt' % (i,))
428 shutil.copy(source, destination)
431 def make_scarf(gerald_dir, lane_list=LANE_LIST):
432 seq = """HWI-EAS229_92_30VNBAAXX:1:1:0:161:NCAATTACACGACGCTAGCCCTAAAGCTATTTCGAGG:E[aaaabb^a\a_^^a[S`ba_WZUXaaaaaaUKPER
433 HWI-EAS229_92_30VNBAAXX:1:1:0:447:NAGATGCGCATTTGAAGTAGGAGCAAAAGATCAAGGT:EUabaab^baabaaaaaaaa^^Uaaaaa\aaaa__`a
434 HWI-EAS229_92_30VNBAAXX:1:1:0:1210:NATAGCCTCTATAGAAGCCACTATTATTTTTTTCTTA:EUa`]`baaaaa^XQU^a`S``S_`J_aaaaaabb^V
435 HWI-EAS229_92_30VNBAAXX:1:1:0:1867:NTGGAGCAGATATAAAAACAGATGGTGACGTTGAAGT:E[^UaaaUaba^aaa^aa^XV\baaLaLaaaaQVXV^
436 HWI-EAS229_92_30VNBAAXX:1:1:0:1898:NAGCTCGTGTCGTGAGATGTTAGGTTAAGTCCTGCAA:EK_aaaaaaaaaaaUZaaZaXM[aaaXSM\aaZ]URE
439 pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
440 f = open(pathname,'w')
444 def make_fastq(gerald_dir, lane_list=LANE_LIST):
445 seq = """@HWI-EAS229:1:2:182:712#0/1
446 AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
447 +HWI-EAS229:1:2:182:712#0/1
448 \\bab_bbaabbababbaaa]]D]bb_baabbab\baa
449 @HWI-EAS229:1:2:198:621#0/1
450 CCCCCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCCCC
451 +HWI-EAS229:1:2:198:621#0/1
452 [aaaaaaa`_`aaaaaaa[`ZDZaaaaaaaaaaaaaa
453 @HWI-EAS229:1:2:209:1321#0/1
454 AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
455 +HWI-EAS229:1:2:209:1321#0/1
456 _bbbbbaaababaabbbbab]D]aaaaaaaaaaaaaa
459 pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
460 f = open(pathname,'w')
464 UNALIGNED_READS = [1,2]
465 UNALIGNED_SAMPLES = [ (1, UNALIGNED_READS, '11111', None, None),
466 (2, UNALIGNED_READS, '11112', None, None),
467 (3, UNALIGNED_READS, '11113', 1, 'ATCACG'),
468 (3, UNALIGNED_READS, '11113', 2, 'CGATGT'),
469 (3, UNALIGNED_READS, '11113', 3, 'TTAGGC'),
470 (4, UNALIGNED_READS, '11114', 6, 'GCCAAT'),
471 (5, UNALIGNED_READS, '11115', 1, 'ATCACG'),
472 (5, UNALIGNED_READS, '11116', 7, 'ACTTGA'),
473 (5, UNALIGNED_READS, '11117', 9, 'GATCAG'),
474 (6, UNALIGNED_READS, '11118', 1, 'ATCACG'),
475 (7, UNALIGNED_READS, '11119', 2, 'CGATGT'),
476 (8, UNALIGNED_READS, '11120', 3, 'TTAGGC'),
477 (1, UNALIGNED_READS, None, None, None),
478 (2, UNALIGNED_READS, None, None, None),
479 (3, UNALIGNED_READS, None, None, None),
480 (4, UNALIGNED_READS, None, None, None),
481 (5, UNALIGNED_READS, None, None, None)]
484 def make_aligned_eland_export(aligned_dir, flowcell_id):
485 summary_source = os.path.join(TESTDATA_DIR, 'sample_summary_1_12.htm')
486 for lane, read, project_id, index_id, index_seq in UNALIGNED_SAMPLES:
487 paths = DemultiplexedPaths(aligned_dir,
493 paths.make_sample_dirs()
494 paths.make_summary_dirs()
495 summary_dest = os.path.join(paths.summary_dir, 'Sample_Summary.htm')
496 shutil.copy(summary_source, summary_dest)
498 body = get_aligned_sample_export(lane, index_seq)
499 for split in ['001','002']:
500 for read in UNALIGNED_READS:
501 suffix = 'R{0}_{1}_export.txt.gz'.format(read, split)
502 pathname = paths.make_test_filename(suffix)
503 stream = gzip.open(pathname, 'w')
508 def make_unaligned_fastqs_1_12(unaligned_dir, flowcell_id):
509 """Create a default mix of unaligned sample files
511 for lane, read, name, index_id, index in UNALIGNED_SAMPLES:
512 make_unaligned_fastq_sample_1_12(unaligned_dir,
520 def make_unaligned_fastq_sample_1_12(unaligned_dir,
528 paths = DemultiplexedPaths(unaligned_dir,
534 paths.make_sample_dirs()
536 sample_seq = get_unaligned_sample_fastq_data(flowcell_id, lane, index_seq)
537 for split in ['001','002']:
539 suffix = 'R{0}_{1}.fastq.gz'.format(read, split)
540 pathname = paths.make_test_filename(suffix)
541 stream = gzip.open(pathname, 'w')
542 stream.write(sample_seq)
545 sheetname = os.path.join(paths.sample_dir, 'SampleSheet.csv')
546 stream = open(sheetname, 'w')
547 stream.write('FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject'+os.linesep)
548 template = '{flowcell},{lane},{id},mm9,{index},Sample #{id},N,PR_indexing,Operator,{sample_project}'+os.linesep
549 stream.write(template.format(flowcell=flowcell_id,
552 index=paths.index_seq,
553 sample_project=paths.sample_project))
557 class DemultiplexedPaths(object):
558 def __init__(self, basedir, flowcell_id, lane, project_id, index_id, index_seq):
559 if lane not in LANE_LIST:
560 raise ValueError("Invalid lane ID: {0}".format(lane))
561 self.basedir = basedir
562 self.flowcell_id = flowcell_id
565 if project_id is None:
568 self.sample_id = 'lane{0}'.format(lane)
569 self.sample_project = 'Undetermined_indices'
570 self.rootname = 'lane{lane}_Undetermined_L00{lane}_'.format(
572 self.project_dir = 'Undetermined_indices'
573 self.sample_dir = 'Sample_lane{lane}'.format(lane=lane)
574 elif index_seq is None:
576 self.sample_id = project_id
577 self.sample_project = '{project_id}'.format(project_id=project_id)
578 self.rootname = '{project_id}_NoIndex_L00{lane}_'.format(
579 project_id=project_id,
581 self.project_dir = 'Project_' + self.sample_project
582 self.sample_dir = 'Sample_{project_id}'.format(
583 project_id=project_id)
585 self.index_seq = index_seq
586 self.sample_id = project_id
587 self.sample_project = '{project_id}_Index{index_id}'.format(
588 project_id=project_id,
590 self.rootname = '{project_id}_{index}_L00{lane}_'.format(
591 project_id=project_id,
594 self.project_dir = 'Project_' + self.sample_project
595 self.sample_dir = 'Sample_{project_id}'.format(
596 project_id=project_id)
598 self.project_dir = os.path.join(self.basedir, self.project_dir)
599 self.sample_dir = os.path.join(self.project_dir, self.sample_dir)
600 self.summary_dir = 'Summary_Stats_{0}'.format(self.flowcell_id)
601 self.summary_dir = os.path.join(self.project_dir, self.summary_dir)
604 def make_sample_dirs(self):
605 if not os.path.isdir(self.project_dir):
606 os.mkdir(self.project_dir)
607 if not os.path.isdir(self.sample_dir):
608 os.mkdir(self.sample_dir)
610 def make_summary_dirs(self):
611 if not os.path.isdir(self.summary_dir):
612 os.mkdir(self.summary_dir)
614 def make_test_filename(self, suffix):
615 filename = self.rootname + suffix
616 pathname = os.path.join(self.sample_dir, filename)
620 print ('index seq: {0}'.format(self.index_seq))
622 print ('project dir: {0}'.format(self.project_dir))
623 print ('sample dir: {0}'.format(self.sample_dir))
624 print ('rootname: {0}'.format(self.rootname))
625 print ('path: {0}'.format(
626 os.path.join(self.project_dir,
628 self.rootname+'R1_001.fastq.gz')))
631 def get_unaligned_sample_fastq_data(flowcell_id, lane, index_seq):
632 seq = """@HWI-ST0787:101:{flowcell}:{lane}:1101:2416:3469 1:Y:0:{index}
633 TCCTTCATTCCACCGGAGTCTGTGGAATTCTCGGGTGCCAAGGAACTCCA
635 CCCFFFFFHHHHHJJJJJJJJJIJJJJJJJJJJJJJJJJIIJJIIJJJJJ
636 @HWI-ST0787:101:{flowcell}:{lane}:1101:2677:3293 1:Y:0:{index}
637 TGGAAATCCATTGGGGTTTCCCCTGGAATTCTCGGGTGCCAAGGAACTCC
639 @CCFF3BDHHHHHIIIIIHHIIIDIIIGIIIEGIIIIIIIIIIIIIIIHH
640 @HWI-ST0787:101:{flowcell}:{lane}:1101:2616:3297 1:Y:0:{index}
641 TAATACTGCCGGGTAATGATGGCTGGAATTCTCGGGTGCCAAGGAACTCC
643 CCCFFFFFHHHHHCGHJJJJJJJJJJJJJJJJJIIJJJJJJJJJIHJJJI
644 @HWI-ST0787:101:{flowcell}:{lane}:1101:2545:3319 1:N:0:{index}
645 TCCTTCATTCCACCGGAGTCTGCTGGAATTCTCGGGTGCCAAGGAACTCC
647 CCCFFFFFHHHFHJGIGHIJHIIGHIGIGIGEHFIJJJIHIJHJIIJJIH
648 """.format(flowcell=flowcell_id, lane=lane, index=index_seq)
651 def get_aligned_sample_export(lane, index_seq):
652 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
653 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
654 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
655 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
656 """.format(lane=lane, index=index_seq)
660 for dirpath, dirnames, filenames in os.walk(root):
661 for filename in filenames:
662 print os.path.join(dirpath, filename)
665 class BaseCallInfo(object):
666 """Provide customization for how to setup the base call mock data
668 def __init__(self, qseq_file, tile_list, basecall_summary):
669 self.qseq_file = qseq_file
670 self.tile_list = tile_list
671 self.basecall_summary = basecall_summary
673 # First generation HiSeq Flowcell
674 ABXX_BASE_CALL_INFO = BaseCallInfo(
675 qseq_file='AA01CCABXX_8_2_2207_qseq.txt',
676 tile_list = HISEQ_TILE_LIST,
677 basecall_summary = 'AA01CCABXX_BustardSummary.xml')