/
run.py
1120 lines (989 loc) · 42.6 KB
/
run.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
# @copyright 2016-2023 Clarity Genomics BVBA
# @copyright 2012-2016 Bonsai Bioinformatics Research Group
# @copyright 2014-2016 Knight Lab, Department of Pediatrics, UCSD, La Jolla
#
# SortMeRNA - next-generation reads filter for metatranscriptomic or total RNA
# This is a free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# SortMeRNA is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with SortMeRNA. If not, see <http://www.gnu.org/licenses/>.
#
# contributors: Jenya Kopylova jenya.kopylov@gmail.com
# Laurent Noé laurent.noe@lifl.fr
# Pierre Pericard pierre.pericard@lifl.fr
# Daniel McDonald wasade@gmail.com
# Mikaël Salson mikael.salson@lifl.fr
# Hélène Touzet helene.touzet@lifl.fr
# Rob Knight robknight@ucsd.edu
'''
file: run.py
created: Aug 12, 2019 Mon
conda install scikit-bio -c conda-forge <- pre-requisites
'''
import os
import sys
import subprocess
import platform
from optparse import OptionParser
import re
import time
import difflib
import shutil
import yaml
from jinja2 import Environment, FileSystemLoader
import gzip
def mock_missing(name):
def init(self, *args, **kwargs):
raise ImportError(
f'The class {name} is not importable; '
f'likely due to it not being installed. '
f'Supposed to be used on a minion running a k8s control node.')
return type(name, (), {'__init__': init})
try:
import pandas
except ImportError:
pandas = mock_missing('pandas')
is_skbio = True
try:
import skbio.io
except (ImportError, OSError) as ex:
print(f'\'import skbio.io\' failed: {ex}')
is_skbio = False
# globals
OS = None
ENV = None # WIN | WSL | LNX_AWS | LNX_TRAVIS
WRK_DIR = None
# define platform
pf = platform.platform()
IS_WIN = 'Windows' in pf
IS_WSL = 'Linux' in pf and 'Microsoft' in pf # Windows Subsystem for Linux (WSL)
IS_LNX = 'Linux' in pf and not 'Microsoft' in pf
OS = 'WIN' if IS_WIN else 'WSL' if IS_WSL else 'LNX' if IS_LNX else None
if not OS:
print(f'Unexpected platform: {pf}')
sys.exit(1)
UHOME = os.environ.get('USERPROFILE') if IS_WIN else os.environ.get('HOME') # not defined for AWS SSM
SMR = 'sortmerna'
SMR_SRC = None # source root dir
SMR_DIST = None # dist root dir
SMR_EXE = None # full path to executable
ZLIB_SRC = None
ZLIB_DIST = None
ROCKS_SRC = None
ROCKS_DIST = None
# no binaries, so always build Release only
RAPID_SRC = None
RAPID_DIST = None
DATA_DIR = None
RUN_DIR = None
OUT_DIR = None
TEST_DATA = None
# base names of the report files
ALI_NAMES = [] # get from test.jinja.yaml + fa/fa + gz/non-gz -> 7 x 4 = 28 names
OTH_NAMES = []
ALI_BASE = 'aligned'
OTH_BASE = 'other'
ALI_FWD_BASE = None # '{}_fwd'.format(ALI_BASE)
ALI_REV_BASE = None # '{}_rev'.format(ALI_BASE)
OTH_FWD_BASE = None # '{}_fwd'.format(OTH_BASE)
OTH_REV_BASE = None # '{}_rev'.format(OTH_BASE)
LOG_BASE = None # '{}.log'.format(ALI_BASE)
DENOVO_BASE = None # '{}_denovo.fasta'.format(ALI_BASE)
OTU_BASE = None # '{}_otus.txt'.format(ALI_BASE)
BLAST_BASE = None # '{}.blast'.format(ALI_BASE)
SAM_BASE = None # '{}.sam'.format(ALI_BASE)
READS_EXT = None
IS_FASTQ = False
IS_PAIRED_IN = False
IS_PAIRED_OUT = False
# output files
LOGF = None
ALIF = None
ALI_FWD = None
ALI_REV = None
OTHF = None
OTH_FWD = None
OTH_REV = None
ALI_REF = None
DENOVOF = None
OTUF = None
BLASTF = None
SAMF = None
# KVDB and index dirs
KVDB_DIR = None
IDX_DIR = None
def run(cmd, cwd=None, capture=False):
'''
'''
ST = '[run]'
ret = {'retcode':0, 'stdout':None, 'stderr':None}
# print compiler version e.g. 'Microsoft (R) C/C++ Optimizing Compiler Version 19.16.27031.1 for x86'
#"%VS_HOME%"\bin\Hostx86\x86\cl.exe
cmds = ' '.join(cmd)
msg = f'{ST} Running: {cmds} in {cwd}' if cwd else f'{ST} Running: {cmds}'
print(msg)
start = time.time()
#print('Running {} in {}'.format(' '.join('{}'.format(xx) for xx in cmd), cwd))
# cmake configure and generate
#kw = {'stdout':subprocess.PIPE, 'stderr':subprocess.PIPE} if capture else {}
try:
if cwd and not os.path.exists(cwd):
os.makedirs(cwd)
proc = subprocess.run(cmd, cwd=cwd, capture_output=capture)
else:
proc = subprocess.run(cmd, capture_output=capture)
ret['retcode'] = proc.returncode
if capture:
ret['stdout'] = proc.stdout
ret['stderr'] = proc.stderr
#proc = subprocess.run(cmd, cwd=build_dir, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
except OSError as err:
print(err)
ret['retcode'] = 1
ret['stderr'] = err
except:
for info in sys.exc_info(): print(info)
ret['retcode'] = 1
ret['stderr'] = sys.exc_info()
rt = time.time() - start
print(f"{ST} run time: {rt}")
return ret
#END cmake_run
def get_diff(fpath0, fpath1):
'''
'''
dlist = []
with open(fpath0, 'rU') as fout:
with open(fpath1, 'rU') as fexpect:
diff = difflib.unified_diff(
fout.readlines(),
fexpect.readlines(),
fromfile='fout',
tofile='fexpect',
)
for line in diff:
dlist.append(line)
if line:
print(line)
return dlist
#END get_diff
def to_lf(ddir):
'''
convert to LF line endings of the data files
NOTE: 'find . -type f -name "*.fasta" -o -name "*.fastq" | xargs dos2unix'
using 'subprocess.run' is problematic because of the pipe.
'''
ST = '[to_lf]'
CRLF = b'\r\n'
LF = b'\n'
for dpath, dnames, fnames in os.walk(ddir):
for fname in fnames:
if fname.endswith('.fasta') or fname.endswith('.fastq'):
fpath = os.path.join(dpath, fname)
print(f'{ST} converting {fpath}')
with open(fpath, 'rb') as infile:
content = infile.read()
content = content.replace(CRLF, LF)
with open(fpath, 'wb') as infile:
infile.write(content)
print('to_lf Done')
#END to_lf
def parse_log(fpath, logd={}):
'''
parse 'aligned.log' to dictionary
:param str fpath 'aligned.log' file
:param dict logd log file structure (test.jinja.yaml:aligned.log)
'''
#logd = {
# 'cmd': ['Command', None],
# 'pid': ['Process pid', None],
# 'params': {'refs': []},
# 'num_reads': ['Total reads =', 0],
# 'results': {
# 'num_hits': ['Total reads passing E-value threshold', 0],
# 'num_fail': ['Total reads failing E-value threshold', 0],
# 'num_denovo': ['Total reads for de novo clustering', 0],
# 'min_len': ['Minimum read length', 0],
# 'max_len': ['Maximum read length', 0],
# 'mean_len': ['Mean read length', 0]
# },
# 'coverage': [],
# 'num_id_cov': ['Total reads passing %%id and %%coverage thresholds', 0],
# 'num_otus': ['Total OTUs', 0],
# 'date': None
#}
with open(fpath) as f_log:
for line in f_log:
if logd['num_reads'][0] in line:
logd['num_reads'][1] = int((re.split(' = ', line)[1]).strip())
elif logd['results']['num_denovo'][0] in line:
logd['results']['num_denovo'][1] = int((re.split(' = ', line)[1]).strip())
elif logd['results']['num_hits'][0] in line:
logd['results']['num_hits'][1] = int((re.split(' = | \(', line)[1]).strip())
elif logd['results']['num_fail'][0] in line:
logd['results']['num_fail'][1] = int((re.split(' = | \(', line)[1]).strip())
elif logd['num_id_cov'][0] in line:
# line: '..thresholds = 44223 (44.22)'
val = line.split('=')[1]
if val: val = val.split()[0].strip()
logd['num_id_cov'][1] = int(val)
elif logd['num_otus'][0] in line:
logd['num_otus'][1] = int((re.split(' = ', line)[1]).strip())
return logd
#END parse_log
def process_smr_opts(args):
'''
:param args list of parameters passed to sortmerna
'''
ST = '[process_smr_opts]'
WDIR = '-workdir'
KVD = '-kvdb'
IDX = '-idx'
ALN = '-aligned'
OTH = '-other'
OUT2 = '-out2'
global KVDB_DIR
global IDX_DIR
global ALI_BASE
global OTH_BASE
global LOGF
global ALIF
global ALI_FWD
global ALI_REV
global OTHF
global OTH_FWD
global OTH_REV
global ALI_REF
global DENOVOF
global OTUF
global BLASTF
global SAMF
global READS_EXT
global IS_FASTQ
global IS_PAIRED_IN
global IS_PAIRED_OUT
global WRK_DIR
is_gz = False
psplit = os.path.splitext(args[args.index('-reads')+1]) # 1.concat.fq.gz -> [1.concat.fq, .gz]
READS_EXT = psplit[1]
if READS_EXT in ['.gz']:
#READS_EXT = os.extsep + args[args.index('-reads')+1].split(os.extsep)[1]
READS_EXT = os.path.splitext(psplit[0])[1]
is_gz = True
IS_FASTQ = READS_EXT[1:] in ['fq', 'fastq']
IS_PAIRED_IN = '-paired_in' in args
IS_PAIRED_OUT = '-paired_out' in args
if ALN in args:
aln_pfx = args[args.index(ALN) + 1]
if not os.path.basename(aln_pfx):
ALIF = os.path.join(aln_pfx, ALI_BASE + READS_EXT) # use default 'aligned'
else:
ALI_BASE = os.path.basename(aln_pfx)
ALIF = os.path.abspath(aln_pfx + READS_EXT)
elif WDIR in args:
wdir = args[args.index(WDIR) + 1]
print('{} \'-workdir\' option was provided. Using workdir: [{}]'.format(ST, os.path.realpath(wdir)))
ALIF = os.path.join(wdir, 'out', ALI_BASE + READS_EXT)
elif WRK_DIR:
ALIF = os.path.join(WRK_DIR, 'out', ALI_BASE + READS_EXT)
elif UHOME:
ALIF = os.path.join(UHOME, 'sortmerna', 'run', 'out', ALI_BASE + READS_EXT)
else:
print(f'{ST} cannot define alignment file')
if OUT2 in args:
ALI_FWD = os.path.join(os.path.dirname(ALIF), ALI_BASE + '_fwd' + READS_EXT)
ALI_REV = os.path.join(os.path.dirname(ALIF), ALI_BASE + '_rev' + READS_EXT)
if OTH in args:
idx = args.index(OTH)
# check idx + 1 no exceeds args length and other options has arg
if idx + 1 < len(args) -1 and args[idx+1][:1] != '-':
oth_pfx = args[idx + 1]
if not os.path.basename(oth_pfx):
OTHF = os.path.join(oth_pfx, OTH_BASE + READS_EXT)
else:
OTH_BASE = os.path.basename(oth_pfx)
OTHF = os.path.abspath(oth_pfx + READS_EXT)
elif ALN in args:
OTHF = os.path.join(os.path.dirname(ALIF), OTH_BASE + READS_EXT) # use the same out dir as ALN
elif WDIR in args:
wdir = args[args.index(WDIR) + 1]
print('{} \'-workdir\' option was provided. Using workdir: [{}]'.format(ST, os.path.realpath(wdir)))
ALIF = os.path.join(wdir, 'out', OTH_BASE + READS_EXT)
else:
OTHF = os.path.join(UHOME, 'sortmerna', 'run', 'out', OTH_BASE + READS_EXT)
if OUT2 in args:
OTH_FWD = os.path.join(os.path.dirname(ALIF), OTH_BASE + '_fwd' + READS_EXT)
OTH_REV = os.path.join(os.path.dirname(ALIF), OTH_BASE + '_rev' + READS_EXT)
if KVD in args:
KVDB_DIR = args[args.index(KVD) + 1]
elif WDIR in args:
KVDB_DIR = os.path.join(args[args.index(WDIR) + 1], 'kvdb')
else:
KVDB_DIR = os.path.join(UHOME, 'sortmerna', 'run', 'kvdb')
if IDX in args:
IDX_DIR = args[args.index(IDX) + 1]
elif WDIR in args:
IDX_DIR = os.path.join(args[args.index(WDIR) + 1], 'idx')
else:
IDX_DIR = os.path.join(UHOME, 'sortmerna', 'run', 'idx')
gzs = '.gz' if is_gz else ''
LOGF = os.path.join(os.path.dirname(ALIF), '{}.log'.format(ALI_BASE))
BLASTF = os.path.join(os.path.dirname(ALIF), '{}.blast{}'.format(ALI_BASE, gzs))
OTUF = os.path.join(os.path.dirname(ALIF), 'otu_map.txt')
DENOVOF = os.path.join(os.path.dirname(ALIF), '{}_denovo.fa'.format(ALI_BASE))
SAMF = os.path.join(os.path.dirname(ALIF), '{}.sam'.format(ALI_BASE))
#END process_smr_opts
def process_blast(**kwarg):
'''
# Check count of reads passing %id and %coverage threshold
# as given in aligned.blast
'''
ST = '[{}]'.format('process_blast')
vald = kwarg.get('validate')
BLAST_ID_COL = 2
BLAST_COV_COL = 13
num_hits_file = 0
n_yid_ycov = 0
n_yid_ncov = 0
n_nid_ycov = 0
n_denovo = 0
has_cov = False
BLAST_PID_PCOV = os.path.join(os.path.dirname(ALIF), 'pid_pcov.blast')
is_dbg_pid_pcov = True
cols = ['qseqid', 'sseqid', 'pident', 'length', 'mismatch', 'gapopen',
'qstart', 'qend', 'sstart', 'send', 'evalue', 'bitscore', 'sseq', 'qcovs']
if os.path.exists(BLASTF):
print(f'{ST} processing : {BLASTF}')
gzs = os.path.basename(BLASTF).split(os.extsep)[-1]
is_gz = gzs == 'gz'
is_use_skbio = False
with open(BLASTF, 'rb') as f_blast:
is_gz = is_gz and (f_blast.read(2) == b'\x1f\x8b')
if is_use_skbio:
# just returns column names - not at all what's expected
for seq in skbio.io.read(BLASTF, format='blast+6', columns=cols, compression='gzip', into=pandas.DataFrame):
num_hits_file += 1
else:
with gzip.open(BLASTF, 'rb') if is_gz else open(BLASTF, 'rb') as f_blast, open(BLAST_PID_PCOV, 'w') as f_pid_pcov:
for lineb in f_blast:
num_hits_file += 1
line = lineb.decode('utf-8')
llist = line.strip().split('\t')
fid = float(llist[BLAST_ID_COL])
is_pass_id = fid >= 97.0
has_cov = len(llist) > BLAST_COV_COL
if has_cov:
fcov = float(llist[BLAST_COV_COL])
is_pass_cov = fcov >= 97.0
if is_pass_id:
if is_pass_cov:
n_yid_ycov += 1
if is_dbg_pid_pcov:
f_pid_pcov.write(line)
else:
n_yid_ncov += 1
elif is_pass_cov:
n_nid_ycov += 1
else:
n_denovo += 1
is_pass_id = False
is_pass_cov = False
bn = os.path.basename(BLASTF)
print(f'{ST} from {bn}: num_hits= {num_hits_file} n_yid_ycov= {n_yid_ycov}'
' n_yid_ncov= {n_yid_ncov} n_nid_ycov= {n_nid_ycov} n_denovo= {n_denovo}')
blastd = vald.get('files', {}).get('aligned.blast')
if blastd:
if blastd.get('n_yid_ycov'):
tmpl = '{} Testing reads passing ID threshold: {}: {} Expected: {}'
print(tmpl.format(ST, os.path.basename(BLASTF), n_yid_ycov, blastd['n_yid_ycov']))
assert n_yid_ycov == blastd['n_yid_ycov'], \
'{} not equals {}'.format(blastd['n_yid_ycov'], n_yid_ycov)
num_recs = blastd.get('num_recs')
if num_recs:
tmpl = '{} Testing num_hits: {}: {} Expected: {}'
print(tmpl.format(ST, os.path.basename(BLASTF), num_hits_file, num_recs))
assert num_hits_file == num_recs, \
'{} not equals {}'.format(num_hits_file, num_recs)
return {
'n_hits' : num_hits_file,
'yid_ycov': n_yid_ycov,
'yid_ncov': n_yid_ncov,
'nid_ycov': n_nid_ycov,
'n_denovo': n_denovo
}
#END process_blast
def dbg_blast(**kwarg):
'''
added 20210323
compare unique read IDs in two blast reports produced using different program versions
cmd: python scripts/run.py --name t0 -f dbg_blast --validate-only
'''
ST = '[{}]'.format('dbg_blast')
rdiff = None
bl_421 = os.path.join(DATA_DIR, 'sortmerna/out/tests/t42/win10_8_16/4-2-1/20210322/aligned.blast')
bl_431 = os.path.join(DATA_DIR, 'sortmerna/out/tests/t42/win10_8_16/4-3-1/20210322/aligned.blast')
srt421 = os.path.join(DATA_DIR, 'sortmerna/out/tests/t42/win10_8_16/4-2-1/20210322/sorted.blast')
srt431 = os.path.join(DATA_DIR, 'sortmerna/out/tests/t42/win10_8_16/4-3-1/20210322/sorted.blast')
if os.path.exists(bl_421) and os.path.exists(bl_431):
with open(bl_421) as f421, open(bl_431) as f431:
l421 = [ line.strip().split('\t')[:2] for line in f421 ]
l431 = [ line.strip().split('\t')[:2] for line in f431 ]
l421.sort(key=lambda rr: int(rr[0].split('.')[-1])) # SRR1635864.8745 -> [SRR1635864, 8745] -> 8745
l431.sort(key=lambda rr: int(rr[0].split('.')[-1]))
with open(srt421, 'w') as sr421, open(srt431, 'w') as sr431:
sr421.write('\n'.join('{}\t{}'.format(x[0], x[1]) for x in l421))
sr431.write('\n'.join('{}\t{}'.format(x[0], x[1]) for x in l431))
#l421 = [ ' '.join(line.strip().split('\t')[:2]) for line in f421 ]
#l431 = [ ' '.join(line.strip().split('\t')[:2]) for line in f431 ]
doset = False
if doset:
rdiff = set(l421) - set(l431)
print('{} rdiff.len= {}'.format(ST, len(rdiff))) # 0
[print(x) for x in list(rdiff)]
#END dbg_blast
def dbg_otu(**kwarg):
'''
'''
ST = '[{}]'.format('dbg_otu')
OTU_READSF = os.path.join(os.path.dirname(ALIF), 'otu_reads.txt')
BLAST_PID_PCOV = os.path.join(os.path.dirname(ALIF), 'pid_pcov.blast')
READS_DIFF = os.path.join(os.path.dirname(ALIF), 'reads_diff.txt')
reads = [] # list of all reads from all groups
blast_reads = []
if os.path.exists(BLAST_PID_PCOV):
with open(BLAST_PID_PCOV) as blastf:
for line in blastf:
lls = line.strip().split('\t')
blast_reads.append(lls[0]) # collect reads
# parse otu groups file
if os.path.exists(OTUF):
num_clusters_file = 0
num_reads_in_clusters_file = 0
with open(OTUF) as f_otus:
for line in f_otus:
num_clusters_file += 1
greads = line.strip().split('\t')[1:] # reads in a group
reads.extend(greads)
num_reads_in_clusters_file += len(greads)
# genreate list of reads
with open(OTU_READSF, 'w') as readsf:
reads.sort(key=lambda rr: int(rr.split('_')[-1]))
reads.sort(key=lambda rr: int(rr.split('_')[0][:-1]))
for read in reads:
readsf.write('{}\n'.format(read))
with open(READS_DIFF, 'w') as diff:
rds = set(blast_reads) - set(reads)
rdsl = list(rds)
rdsl.sort(key=lambda rr: int(rr.split('_')[-1]))
rdsl.sort(key=lambda rr: int(rr.split('_')[0][:-1]))
for rd in rdsl:
diff.write('{}\n'.format(rd))
#END dbg_otu
def validate_otu(**kwarg):
'''
:param dict kwarg test configuration see 'test.jinja.yaml'
:param dict kwarg[logd] parsed aligned.log data see 'parse_log(LOGF)'
'''
ST = '[{}]'.format('validate_otu')
vald = kwarg.get('validate')
logd = kwarg.get('logd') or parse_log(LOGF)
# parse otu groups file
if os.path.exists(OTUF):
num_clusters_file = 0
num_reads_in_clusters_file = 0
with open(OTUF) as f_otus:
for line in f_otus:
num_clusters_file += 1
num_reads_in_clusters_file += (len(line.strip().split('\t'))-1)
print('{} num groups in OTU file {} , expected {}'.format(ST, num_clusters_file, logd['num_otus'][1]))
assert logd['num_otus'][1] == num_clusters_file, \
'{} not equals {}'.format(logd['num_otus'][1], num_clusters_file)
print('{} count of reads in OTU file {} , expected {}'.format(ST, num_reads_in_clusters_file, logd['num_id_cov'][1]))
assert logd['num_id_cov'][1] == num_reads_in_clusters_file, \
'{} not equals {}'.format(logd['num_id_cov'][1], num_reads_in_clusters_file)
# verify count of groups in the aligned.log is the same as specified in configuration validate data
if logd.get('num_otus') and vald.get('num_cluster'):
assert logd['num_otus'][1] in vald['num_cluster'], \
'{} not in {}'.format(logd['num_otus'][1], vald['num_cluster'])
#END validate_otu
def validate_log(logd, ffd):
'''
:param dict logd
:param dict ffd files data as in test.jinja.yaml:<test_name>:validate:files
'''
ST = '[validate_log]'
# aligned.log :
# verify the total number of reads in aligned.log vs the number in the validation spec
n_vald = ffd.get('aligned.log', {}).get('num_reads')
n_logd = logd['num_reads'][1]
if n_vald:
print('{} testing num_reads: {} Expected: {}'.format(ST, n_logd, n_vald))
assert n_vald == n_logd, '{} not equals {}'.format(n_vald, n_logd)
# verify number of hits
n_vald = ffd.get('aligned.log', {}).get('num_hits')
n_logd = logd['results']['num_hits'][1]
if n_vald:
print('{} testing num_hits: {} Expected: {}'.format(ST, n_logd, n_vald))
assert n_vald == n_logd, '{} not equals {}'.format(n_vald, n_logd)
# verify number of misses
n_vald = ffd.get('aligned.log', {}).get('num_fail')
n_logd = logd['results']['num_fail'][1]
if n_vald:
print('{} testing num_fail: {} Expected: {}'.format(ST, n_logd, n_vald))
assert n_vald == n_logd, '{} not equals {}'.format(n_vald, n_logd)
# verify count of COV+ID
n_vald = ffd.get('aligned.log', {}).get('n_yid_ycov')
n_logd = logd['num_id_cov'][1]
if n_vald:
print('{} testing n_yid_ycov: {} Expected: {}'.format(ST, n_logd, n_vald))
assert n_vald == n_logd, '{} not equals {}'.format(n_vald, n_logd)
# verify count of OUT groups
n_vald = ffd.get('aligned.log', {}).get('num_groups')
n_logd = logd['num_otus'][1]
if n_vald:
print(f'{ST} testing num_groups: {n_logd} Expected: {n_vald}')
assert n_vald == n_logd, '{} not equals {}'.format(n_vald, n_logd)
# verify count of de-novo reads
n_vald = ffd.get('aligned.log', {}).get('n_denovo')
n_logd = logd['results']['num_denovo'][1]
if n_vald:
print(f'{ST} testing n_denovo: {n_logd} Expected: {n_vald}')
assert n_vald == n_logd, '{} not equals {}'.format(n_vald, n_logd)
#END validate_log
def process_output(name, **kwarg):
'''
:param str name test name e.g. t0
:param dict test configuration see 'test.jinja'
'''
ST = '[process_output]'
global is_skbio
log_struct = kwarg.get('aligned.log')
vald = kwarg.get(name, {}).get('validate')
#cmdd = kwarg.get('cmd')
if not vald:
print('{} validation info not provided'.format(ST))
return
logd = parse_log(LOGF, log_struct)
ffd = vald.get('files')
if ffd and isinstance(ffd, dict):
for ff, vv in ffd.items():
print('{} {}'.format(ST, ff))
# Check aligned/other reads count
# aligned/other files only specify read count in the test validation data
if isinstance(vv, int):
ffp = os.path.join(os.path.dirname(ALIF), ff) # file path
count = 0
assert os.path.exists(ffp), '{} does not exists: {}'.format(ST, ffp)
if ff == 'otu_map.txt':
with open(ffp) as ffs:
for line in ffs:
count += 1
print('{} testing count of groups in {}: {} Expected: {}'.format(ST, ff, count, vv))
assert count == vv, '{} not equals {}'.format(count, vv)
continue
if is_skbio:
if IS_FASTQ:
for seq in skbio.io.read(ffp, format='fastq', variant=vald.get('variant')):
count += 1
else:
fmt = 'fasta' if READS_EXT[1:] in ['fasta', 'fa'] else READS_EXT[1:]
for seq in skbio.io.read(ffp, format=fmt):
count += 1
print('{} Testing count of reads in {}: {} Expected: {}'.format(ST, ff, count, vv))
assert count == vv, '{} not equals {}'.format(count, vv)
elif ff == 'aligned.log':
validate_log(logd, ffd)
elif 'aligned.blast' in ff:
test_cfg = kwarg.get(name, {})
process_blast(**test_cfg)
#END process_output
def t0(datad, ret={}, **kwarg):
'''
:param datad Data directory
:param outd results output directory
'''
ST = '[t0:{}]'.format(kwarg.get('name'))
print('{} Validating ...'.format(ST))
BLAST_EXPECTED = os.path.join(datad, 't0_expected_alignment.blast')
dlist = []
with open(BLASTF, 'r') as fout:
with open(BLAST_EXPECTED, 'r') as fexpect:
diff = difflib.unified_diff(
fout.readlines(),
fexpect.readlines(),
fromfile='fout',
tofile='fexpect',
)
for line in diff:
dlist.append(line)
if line:
print(line, end='')
assert len(dlist) == 0
print("{} Done".format(ST))
#END t0
def t2(datad, ret={}, **kwarg):
'''
:param datad Data directory
:param kwargs validation args
Test the following case for alignment:
beginning from align_ref_start = 0 and align_que_start = X, the read finishes
before the end of the reference
ref |----------------|
que |------------------------|
LIS |-----|
^
align_que_start
'''
ST = '[t2:{}]'.format(kwarg.get('name'))
print('{} Validating ...'.format(ST))
vald = kwarg['validate']
actual_alignment = []
with open(BLASTF) as afile:
for line in afile:
actual_alignment = line.strip().split('\t')
assert len(vald['expected']) == len(actual_alignment)
assert sorted(vald['expected']) == sorted(actual_alignment)
#a = set(expected_alignment) & set(actual_alignment)
print("{} Done".format(ST))
#END t2
def t3(datad, ret={}, **kwarg):
'''
:param datad Data directory
:param outd results output directory
:param kwargs validation args
test_environmental_output
Test outputting FASTA file for de novo clustering
using environmental data.
Conditions: input FASTA file is processed in
one mapped section.
'''
ST = '[t3:{}]'.format(kwarg.get('name'))
print('{} Validating ...'.format(ST))
global is_skbio
logd = parse_log(LOGF)
vald = kwarg.get('validate')
cmdd = kwarg.get('cmd')
assert logd['results']['num_hits'][1] == vald['num_hits']
process_blast(**kwarg)
# sort order (descending/ascending) of candidate references (alignment.cpp)
is_refs_descending = False
# 'Total OTUs' in aligned.log has to be equal 'num_groups' in test.jinja.yaml
if is_refs_descending:
assert logd['num_otus'][1] == vald['num_groups'][0] # originally
else:
assert logd['num_otus'][1] == vald['num_groups'][1], \
'num_otus = {} != num_groups = {} expected'.format(logd['num_otus'][1], vald['num_groups'][1])
# OTU file contains one line per OTU group, so the number of lines
# has to be equal 'Total OTUs' in aligned.log
with open(OTUF) as f_otumap:
num_clusters_file = sum(1 for line in f_otumap)
assert logd['num_otus'][1] == num_clusters_file, \
'num_otus = {} != {}:num_otus = {}'.format(logd['num_otus'][1],
OTU_BASE, num_clusters_file)
# number of reads in aligned_denovo.fasta has to be equal the
# 'Total reads for de novo clustering' in aligned.log
n_denovo_file = 0
if is_skbio:
for seq in skbio.io.read(DENOVOF, format='fasta'):
n_denovo_file += 1
assert logd['results']['num_denovo'][1] == n_denovo_file, \
'num_denovo = {} != {}:num_denovo = {}'.format(\
logd['results']['num_denovo'][1], DENOVO_BASE, n_denovo_file)
print("{} Done".format(ST))
#END t3
def t4(datad, ret={}, **kwarg ):
'''
count idx files
'''
ST = '[t4:{}]'.format(kwarg.get('name'))
vald = kwarg.get('validate')
if IS_WIN:
sfx = vald.get('idx_sfx_win')
else:
sfx = vald.get('idx_sfx_lin')
idx_count = 0
idx_count_expect = vald.get('num_idx') * 3 + 1
if os.path.exists(IDX_DIR):
idx_count = len([fn for fn in os.listdir(IDX_DIR) if str(sfx) in fn])
print('{} Expected number of index files: {} Actual number: {}'.format(ST, idx_count_expect, idx_count))
assert idx_count_expect == idx_count
#END t4
def t9(datad, ret={}, **kwarg):
'''
:param datad data directory
:param dict ret results of the aignment
test_output_all_alignments_f_rc
'''
ST = '[t9:{}]'.format(kwarg.get('name'))
print(f'{ST} Validating ...')
vald = kwarg.get('validate')
sam_alignments = []
with open(SAMF) as aligned_f:
for line in aligned_f:
if line.startswith('@'):
continue
alignment = line.strip().split("\t")
sam_alignments.append(alignment)
assert len(vald['sam_alignments_expected']) == len(sam_alignments)
for alignment in vald['sam_alignments_expected']:
assert alignment in sam_alignments
print(f"{ST} done")
#END t9
def t10(datad, ret={}, **kwarg):
'''
:param str datad data directory
:param dict ret results of the aignment
test_ref_shorter_than_seed
'''
ST = '[t10:{}]'.format(kwarg.get('name'))
print(f'{ST} validating ...'.format)
vald = kwarg.get('validate')
if ret and ret.get('retcode'):
assert ret['retcode'] == 1
assert vald['err_msg'] in ret['stderr'].decode("utf-8")
print("{ST} done")
#END t10
def t11(datad, ret={}, **kwarg):
'''
@param smrexe sortmerna.exe path
@param datad Data directory
@param outd results output directory
Test on simulated data,
10000 reads with 1% error (--aligned),
10000 reads with 10% error (de novo),
10000 reads random (--other)
Conditions: reference index and input
query FASTA file both processed as one
section.
'''
ST = '[t11:{}]'.format(kwarg.get('name'))
print('{} Validating ...'.format(ST))
if ret and ret.get('retcode'):
print('ERROR running alignemnt. Return code: {}'.format(ret['retcode']))
print(ret['stdout'])
print(ret['stderr'])
sys.exit(1)
else:
process_output(**kwarg)
print("{} Done".format(ST))
#END t11
def t12(datad, ret={}, **kwarg):
'''
@param smrexe sortmerna.exe path
@param datad Data directory
@param outd results output directory
Test on simulated data,
10000 reads with 1% error (--aligned),
10000 reads with 10% error (de novo),
10000 reads random (--other)
Conditions: reference index and input
query FASTA file both processed as one
section.
'''
ST = '[t12:{}]'.format(kwarg.get('name'))
print('{} Validating ...'.format(ST))
if ret and ret.get('retcode'):
print('ERROR running alignemnt. Return code: {}'.format(ret['retcode']))
print(ret['stdout'])
print(ret['stderr'])
sys.exit(1)
else:
process_output(**kwarg)
print("{} Done".format(ST))
#END t12
def t17(datad, ret={}, **kwarg):
'''
:param name sortmerna.exe path
:param datad Data directory
:param outd results output directory
:param capture Capture output
'''
ST = '[t17:{}]'.format(kwarg.get('name'))
print(f'{ST} TODO: implement')
logd = parse_log(LOGF)
print("{ST} done")
#END t17
def set_file_names(basenames, is_other=False):
'''
:param list basenames list of basenames as in test.jinja,yaml:aligned.names
:param bool is_other flag aligned (default) | other files
'''
global ALI_NAMES
if __name__ == "__main__":
'''
$env:path="$env:userprofile/a1/code/sortmerna/dist/bin;$env:path"; &python scripts/run.py -n t1
python scripts/run.py -n t1 --smr-exe=dist/bin/sortmerna.exe
python scripts/run.py -n t15 --smr-exe=dist/bin/sortmerna.exe --data-dir=../../data
python scripts/run.py -n t0 -v [--capture] [--validate-only]
python scripts/run.py --name t12 -f process_otu --validate-only -d 2
python scripts/run.py --name t0 -f dbg_blast --validate-only
python /media/sf_a01_code/sortmerna/scripts/run.py --name t6 --envn LNX_VBox_Ubuntu_1804
python /mnt/c/Users/biocodz/a01_code/sortmerna/tests/run.py --name t0 --winhome /mnt/c/Users/biocodz [--capture]
|_ on WSL
'''
ST = '[run.py:__main__]'
#import pdb; pdb.set_trace()
is_opts_ok = True
# process options
optpar = OptionParser()
optpar.add_option('-n', '--name', dest='name', help='Test to run e.g. t0 | t1 | t2 | to_lf | to_crlf | all')
optpar.add_option('-f', '--func', dest='func', help='function to run: process_otu | ')
optpar.add_option('-c', '--clean', action="store_true", help='clean Work directory and exit. Requires \'--name\'')
optpar.add_option('-d', '--dbg_level', dest="dbg_level", help='debug level 0 | 1 | 2')
optpar.add_option('--btype', dest='btype', default='release', help = 'Build type: release | debug')
optpar.add_option('--pt_smr', dest='pt_smr', default='t1', help = 'Sortmerna Linkage type t1 | t2 | t3')
optpar.add_option('--winhome', dest='winhome', help='when running on WSL - home directory on Windows side e.g. /mnt/c/Users/XX')
optpar.add_option('--capture', action="store_true", help='Capture output. By default prints to stdout')
optpar.add_option('-v', '--validate-only', action="store_true", help='Only perform validation. Assumes aligement already done')
optpar.add_option('--config', dest='config', help='Tests configuration file.')
optpar.add_option('--env', dest='envfile', help='Environment variables')
optpar.add_option('-e','--envn', dest='envname', help=('Name of environment: WIN | WSL '
'| LNX_AWS | LNX_TRAVIS | LNX_VBox_Ubuntu_1804 | ..'))
optpar.add_option('-w', '--workdir', dest='workdir', help='Environment variables')
optpar.add_option('--threads', dest='threads', help='Number of threads to use')
optpar.add_option('--index', dest='index', help='Index option 0 | 1 | 2')
optpar.add_option('-t', '--task', dest='task', help='Processing task 0 | 1 | 2 | 3 | 4')
optpar.add_option('--smr-exe', dest='smr_exe', help='path to sortmerna executable. Abs or relative')
optpar.add_option('--data-dir', dest='data_dir', help='path to the data. Abs or relative')
(opts, args) = optpar.parse_args()
# process configuration
script_dir = os.path.dirname(os.path.realpath(__file__)) # directory where this script is located
SMR_SRC = os.path.dirname(script_dir)
DATA_DIR = opts.data_dir
print(f'{ST} smr source dir: {SMR_SRC} script dir: {script_dir}')
# check env.yaml. If no env file specified, try the current directory
env_yaml = os.path.join(script_dir, 'env.jinja') if not opts.envfile else opts.envfile
if not os.path.exists(env_yaml):
print('{} No environment config file found. Please, provide one using \'--env\' option'.format(ST))
sys.exit(1)
else:
# load properties from env.yaml
print('{} Using Environment configuration file: {}'.format(ST, env_yaml))
#with open(env_yaml, 'r') as envh:
# env = yaml.load(envh, Loader=yaml.FullLoader)
env_jj = Environment(loader=FileSystemLoader(os.path.dirname(env_yaml)), trim_blocks=True, lstrip_blocks=True)
env_template = env_jj.get_template(os.path.basename(env_yaml))
# render jinja template env.jinja.yaml
vars = {'UHOME': UHOME}
if IS_WSL: vars['WINHOME'] = opts.winhome
env_str = env_template.render(vars)
env = yaml.load(env_str, Loader=yaml.FullLoader)
# check test.jinja
cfgfile = os.path.join(script_dir, 'test.jinja') if not opts.config else opts.config
if not os.path.exists(cfgfile):
print('{} No build configuration template found. Please, provide one using \'--config\' option'.format(ST))
sys.exit(1)