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
|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2011-2013, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# -----------------------------------------------------------------------------
__author__ = "Jai Ram Rideout"
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = ["Jai Ram Rideout", "Daniel McDonald",
"Jorge Cañardo Alastuey"]
__license__ = "BSD"
__url__ = "http://biom-format.org"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
import os
import json
from unittest import TestCase, main
from shutil import copy
import numpy.testing as npt
from biom.cli.table_validator import TableValidator
from biom.util import HAVE_H5PY
if HAVE_H5PY:
import h5py
class TableValidatorTests(TestCase):
def setUp(self):
"""Set up data for use in unit tests."""
self.cmd = TableValidator()
self.min_sparse_otu = json.loads(min_sparse_otu)
self.rich_sparse_otu = json.loads(rich_sparse_otu)
self.rich_dense_otu = json.loads(rich_dense_otu)
self.min_dense_otu = json.loads(min_dense_otu)
self.to_remove = []
cur_path = os.path.split(os.path.abspath(__file__))[0]
examples_path = os.path.join(cur_path.rsplit('/', 2)[0], 'examples')
self.hdf5_file_valid = os.path.join(examples_path,
'min_sparse_otu_table_hdf5.biom')
self.hdf5_file_valid_md = os.path.join(examples_path,
('rich_sparse_otu_table_hdf5'
'.biom'))
def tearDown(self):
for f in self.to_remove:
os.remove(f)
@npt.dec.skipif(HAVE_H5PY == False, msg='H5PY is not installed')
def test_valid_hdf5_metadata_v210(self):
exp = {'valid_table': True, 'report_lines': []}
obs = self.cmd(table=self.hdf5_file_valid,
format_version='2.1')
self.assertEqual(obs, exp)
obs = self.cmd(table=self.hdf5_file_valid_md,
format_version='2.1')
self.assertEqual(obs, exp)
@npt.dec.skipif(HAVE_H5PY == False, msg='H5PY is not installed')
def test_valid_hdf5_metadata_v200(self):
pass # omitting, not a direct way to test at this time using the repo
@npt.dec.skipif(HAVE_H5PY == False, msg='H5PY is not installed')
def test_valid_hdf5(self):
"""Test a valid HDF5 table"""
exp = {'valid_table': True,
'report_lines': []}
obs = self.cmd(table=self.hdf5_file_valid)
self.assertEqual(obs, exp)
@npt.dec.skipif(HAVE_H5PY == False, msg='H5PY is not installed')
def test_invalid_hdf5(self):
"""Test an invalid HDF5 table"""
exp = {'valid_table': False,
'report_lines': ["Missing attribute: 'creation-date'"]}
copy(self.hdf5_file_valid, 'invalid.hdf5')
self.to_remove.append('invalid.hdf5')
f = h5py.File('invalid.hdf5', 'a')
del f.attrs['creation-date']
f.close()
obs = self.cmd(table='invalid.hdf5')
self.assertEqual(obs, exp)
def test_valid(self):
"""Correctly validates a table that is indeed... valid."""
exp = {'valid_table': True, 'report_lines': []}
f = open('valid_test1', 'w')
f.write(json.dumps(self.min_sparse_otu))
f.close()
self.to_remove.append('valid_test1')
obs = self.cmd(table='valid_test1')
self.assertEqual(obs, exp)
f = open('valid_test2', 'w')
f.write(json.dumps(self.rich_sparse_otu))
f.close()
self.to_remove.append('valid_test2')
obs = self.cmd(table='valid_test2')
self.assertEqual(obs, exp)
# Soldier, report!!
f = open('valid_test3', 'w')
f.write(json.dumps(self.rich_sparse_otu))
f.close()
self.to_remove.append('valid_test3')
obs = self.cmd(table='valid_test3', detailed_report=True)
self.assertTrue(obs['valid_table'])
self.assertTrue(len(obs['report_lines']) > 0)
def test_invalid(self):
"""Correctly invalidates a table that is... invalid."""
del self.min_sparse_otu['date']
exp = {'valid_table': False, 'report_lines': ["Missing field: 'date'"]}
f = open('invalid_test1', 'w')
f.write(json.dumps(self.min_sparse_otu))
f.close()
self.to_remove.append('invalid_test1')
obs = self.cmd(table='invalid_test1')
self.assertEqual(obs, exp)
self.rich_dense_otu['shape'][1] = 42
exp = {'valid_table': False,
'report_lines': ['Incorrect number of cols: [0, 0, 1, 0, 0, 0]',
"Number of columns in 'columns' is not equal "
"to 'shape'"]}
f = open('invalid_test2', 'w')
f.write(json.dumps(self.rich_dense_otu))
f.close()
self.to_remove.append('invalid_test2')
obs = self.cmd(table='invalid_test2')
self.assertEqual(obs, exp)
def test_valid_format_url(self):
"""validates format url"""
table = self.min_sparse_otu
obs = self.cmd._valid_format_url(table)
self.assertTrue(len(obs) == 0)
table['format_url'] = 'foo'
obs = self.cmd._valid_format_url(table)
self.assertTrue(len(obs) > 0)
def test_valid_format(self):
"""Should match format string"""
table = self.min_sparse_otu
self.cmd._format_version = '1.0.0'
obs = self.cmd._valid_format(table)
self.assertTrue(len(obs) == 0)
table['format'] = 'foo'
obs = self.cmd._valid_format(table)
self.assertTrue(len(obs) > 0)
def test_valid_type(self):
"""Should be valid table type"""
table = self.min_sparse_otu
table['type'] = 'otu table' # should not be case sensitive
obs = self.cmd._valid_type(table)
self.assertTrue(len(obs) == 0)
table['type'] = 'Pathway table'
obs = self.cmd._valid_type(table)
self.assertTrue(len(obs) == 0)
table['type'] = 'Function table'
obs = self.cmd._valid_type(table)
self.assertTrue(len(obs) == 0)
table['type'] = 'Ortholog table'
obs = self.cmd._valid_type(table)
self.assertTrue(len(obs) == 0)
table['type'] = 'Gene table'
obs = self.cmd._valid_type(table)
self.assertTrue(len(obs) == 0)
table['type'] = 'Metabolite table'
obs = self.cmd._valid_type(table)
self.assertTrue(len(obs) == 0)
table['type'] = 'OTU table'
obs = self.cmd._valid_type(table)
self.assertTrue(len(obs) == 0)
table['type'] = 'Taxon table'
obs = self.cmd._valid_type(table)
self.assertTrue(len(obs) == 0)
table['type'] = 'foo'
obs = self.cmd._valid_type(table)
self.assertTrue(len(obs) > 0)
def test_valid_generated_by(self):
"""Should have some string for generated by"""
table = self.min_sparse_otu
obs = self.cmd._valid_generated_by(table)
self.assertTrue(len(obs) == 0)
table['generated_by'] = None
obs = self.cmd._valid_generated_by(table)
self.assertTrue(len(obs) > 0)
def test_valid_nullable_id(self):
"""Should just work."""
pass
def test_valid_metadata(self):
"""Can be nullable or an object"""
table = self.min_sparse_otu
table['rows'][2]['metadata'] = None
obs = self.cmd._valid_metadata(table['rows'][2])
self.assertTrue(len(obs) == 0)
table['rows'][2]['metadata'] = {10: 20}
obs = self.cmd._valid_metadata(table['rows'][2])
self.assertTrue(len(obs) == 0)
table['rows'][2]['metadata'] = ""
obs = self.cmd._valid_metadata(table['rows'][2])
self.assertTrue(len(obs) > 0)
table['rows'][2]['metadata'] = "asdasda"
obs = self.cmd._valid_metadata(table['rows'][2])
self.assertTrue(len(obs) > 0)
table['rows'][2]['metadata'] = [{'a': 'b'}, {'c': 'd'}]
obs = self.cmd._valid_metadata(table['rows'][2])
self.assertTrue(len(obs) > 0)
def test_valid_matrix_type(self):
"""Make sure we have a valid matrix type"""
obs = self.cmd._valid_matrix_type(self.min_dense_otu)
self.assertTrue(len(obs) == 0)
obs = self.cmd._valid_matrix_type(self.min_sparse_otu)
self.assertTrue(len(obs) == 0)
table = self.min_dense_otu
table['matrix_type'] = 'spARSe'
obs = self.cmd._valid_matrix_type(table)
self.assertTrue(len(obs) > 0)
table['matrix_type'] = 'sparse_asdasd'
obs = self.cmd._valid_matrix_type(table)
self.assertTrue(len(obs) > 0)
def test_valid_matrix_element_type(self):
"""Make sure we have a valid matrix type"""
table = self.min_sparse_otu
obs = self.cmd._valid_matrix_element_type(table)
self.assertTrue(len(obs) == 0)
table['matrix_element_type'] = u'int'
obs = self.cmd._valid_matrix_element_type(table)
self.assertTrue(len(obs) == 0)
table['matrix_element_type'] = 'float'
obs = self.cmd._valid_matrix_element_type(table)
self.assertTrue(len(obs) == 0)
table['matrix_element_type'] = u'float'
obs = self.cmd._valid_matrix_element_type(table)
self.assertTrue(len(obs) == 0)
table['matrix_element_type'] = 'str'
obs = self.cmd._valid_matrix_element_type(table)
self.assertTrue(len(obs) == 0)
table['matrix_element_type'] = u'str'
obs = self.cmd._valid_matrix_element_type(table)
self.assertTrue(len(obs) == 0)
table['matrix_element_type'] = 'obj'
obs = self.cmd._valid_matrix_element_type(table)
self.assertTrue(len(obs) > 0)
table['matrix_element_type'] = u'asd'
obs = self.cmd._valid_matrix_element_type(table)
self.assertTrue(len(obs) > 0)
def test_valid_datetime(self):
"""Make sure we have a datetime stamp"""
table = self.min_sparse_otu
obs = self.cmd._valid_datetime(table)
self.assertTrue(len(obs) == 0)
table['date'] = "1999-11-11T10:11:12"
obs = self.cmd._valid_datetime(table)
self.assertTrue(len(obs) == 0)
def test_valid_sparse_data(self):
"""Takes a sparse matrix field and validates"""
table = self.min_sparse_otu
obs = self.cmd._valid_sparse_data(table)
self.assertTrue(len(obs) == 0)
# incorrect type
table['matrix_element_type'] = 'float'
obs = self.cmd._valid_sparse_data(table)
self.assertTrue(len(obs) > 0)
# not balanced
table['matrix_element_type'] = 'int'
table['data'][5] = [0, 10]
obs = self.cmd._valid_sparse_data(table)
self.assertTrue(len(obs) > 0)
# odd type for index
table['data'][5] = [1.2, 5, 10]
obs = self.cmd._valid_sparse_data(table)
self.assertTrue(len(obs) > 0)
def test_valid_dense_data(self):
"""Takes a dense matrix field and validates"""
table = self.min_dense_otu
obs = self.cmd._valid_dense_data(table)
self.assertTrue(len(obs) == 0)
# incorrect type
table['matrix_element_type'] = 'float'
obs = self.cmd._valid_dense_data(table)
self.assertTrue(len(obs) > 0)
# not balanced
table['matrix_element_type'] = 'int'
table['data'][1] = [0, 10]
obs = self.cmd._valid_dense_data(table)
self.assertTrue(len(obs) > 0)
# bad type in a field
table['data'][1] = [5, 1, 0, 2.3, 3, 1]
obs = self.cmd._valid_dense_data(table)
self.assertTrue(len(obs) > 0)
def test_valid_shape(self):
"""validates shape information"""
obs = self.cmd._valid_shape(self.min_sparse_otu)
self.assertTrue(len(obs) == 0)
obs = self.cmd._valid_shape(self.rich_sparse_otu)
self.assertTrue(len(obs) == 0)
bad_shape = self.min_sparse_otu.copy()
bad_shape['shape'] = ['asd', 10]
obs = self.cmd._valid_shape(bad_shape)
self.assertTrue(len(obs) > 0)
def test_valid_rows(self):
"""validates rows: field"""
table = self.rich_dense_otu
obs = self.cmd._valid_rows(table)
self.assertTrue(len(obs) == 0)
table['rows'][0]['id'] = ""
obs = self.cmd._valid_rows(table)
self.assertTrue(len(obs) > 0)
table['rows'][0]['id'] = None
obs = self.cmd._valid_rows(table)
self.assertTrue(len(obs) > 0)
del table['rows'][0]['id']
obs = self.cmd._valid_rows(table)
self.assertTrue(len(obs) > 0)
table['rows'][0]['id'] = 'asd'
table['rows'][0]['metadata'] = None
obs = self.cmd._valid_rows(table)
self.assertTrue(len(obs) == 0)
# since this is an OTU table, metadata is a required key
del table['rows'][0]['metadata']
obs = self.cmd._valid_rows(table)
self.assertTrue(len(obs) > 0)
def test_valid_columns(self):
"""validates table:columns: fields"""
table = self.rich_dense_otu
obs = self.cmd._valid_columns(table)
self.assertTrue(len(obs) == 0)
table['columns'][0]['id'] = ""
obs = self.cmd._valid_columns(table)
self.assertTrue(len(obs) > 0)
table['columns'][0]['id'] = None
obs = self.cmd._valid_columns(table)
self.assertTrue(len(obs) > 0)
del table['columns'][0]['id']
obs = self.cmd._valid_columns(table)
self.assertTrue(len(obs) > 0)
table['columns'][0]['id'] = 'asd'
table['columns'][0]['metadata'] = None
obs = self.cmd._valid_columns(table)
self.assertTrue(len(obs) == 0)
# since this is an OTU table, metadata is a required key
del table['columns'][0]['metadata']
obs = self.cmd._valid_columns(table)
self.assertTrue(len(obs) > 0)
def test_valid_data(self):
"""validates data: fields"""
# the burden of validating data is passed on to valid_sparse_data
# and valid_dense_data
table = self.rich_sparse_otu
obs = self.cmd._valid_data(table)
self.assertTrue(len(obs) == 0)
table['matrix_type'] = 'foo'
obs = self.cmd._valid_data(table)
self.assertTrue(len(obs) > 0)
rich_sparse_otu = """{
"id":null,
"format": "1.0.0",
"format_url": "http://biom-format.org",
"type": "OTU table",
"generated_by": "QIIME revision XYZ",
"date": "2011-12-19T19:00:00",
"rows":[{"id":"GG_OTU_1",
"metadata":{"taxonomy":["k__Bacteria",
"p__Proteobacteria",
"c__Gammaproteobacteria",
"o__Enterobacteriales",
"f__Enterobacteriaceae",
"g__Escherichia",
"s__"]}},
{"id":"GG_OTU_2",
"metadata":{"taxonomy":["k__Bacteria",
"p__Cyanobacteria",
"c__Nostocophycideae",
"o__Nostocales",
"f__Nostocaceae",
"g__Dolichospermum",
"s__"]}},
{"id":"GG_OTU_3",
"metadata":{"taxonomy":["k__Archaea",
"p__Euryarchaeota",
"c__Methanomicrobia",
"o__Methanosarcinales",
"f__Methanosarcinaceae",
"g__Methanosarcina",
"s__"]}},
{"id":"GG_OTU_4",
"metadata":{"taxonomy":["k__Bacteria",
"p__Firmicutes",
"c__Clostridia",
"o__Halanaerobiales",
"f__Halanaerobiaceae",
"g__Halanaerobium",
"s__Halanaerobiumsaccharolyticum"]}},
{"id":"GG_OTU_5",
"metadata":{"taxonomy":["k__Bacteria",
"p__Proteobacteria",
"c__Gammaproteobacteria",
"o__Enterobacteriales",
"f__Enterobacteriaceae",
"g__Escherichia",
"s__"]}}
],
"columns":[
{"id":"Sample1", "metadata":{
"BarcodeSequence":"CGCTTATCGAGA",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"gut",
"Description":"human gut"}},
{"id":"Sample2", "metadata":{
"BarcodeSequence":"CATACCAGTAGC",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"gut",
"Description":"human gut"}},
{"id":"Sample3", "metadata":{
"BarcodeSequence":"CTCTCTACCTGT",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"gut",
"Description":"human gut"}},
{"id":"Sample4", "metadata":{
"BarcodeSequence":"CTCTCGGCCTGT",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"skin",
"Description":"human skin"}},
{"id":"Sample5", "metadata":{
"BarcodeSequence":"CTCTCTACCAAT",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"skin",
"Description":"human skin"}},
{"id":"Sample6", "metadata":{
"BarcodeSequence":"CTAACTACCAAT",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"skin",
"Description":"human skin"}}
],
"matrix_type": "sparse",
"matrix_element_type": "int",
"shape": [5, 6],
"data":[[0,2,1],
[1,0,5],
[1,1,1],
[1,3,2],
[1,4,3],
[1,5,1],
[2,2,1],
[2,3,4],
[2,5,2],
[3,0,2],
[3,1,1],
[3,2,1],
[3,5,1],
[4,1,1],
[4,2,1]
]
}"""
min_sparse_otu = """{
"id":null,
"format": "1.0.0",
"format_url": "http://biom-format.org",
"type": "OTU table",
"generated_by": "QIIME revision XYZ",
"date": "2011-12-19T19:00:00",
"rows":[
{"id":"GG_OTU_1", "metadata":null},
{"id":"GG_OTU_2", "metadata":null},
{"id":"GG_OTU_3", "metadata":null},
{"id":"GG_OTU_4", "metadata":null},
{"id":"GG_OTU_5", "metadata":null}
],
"columns": [
{"id":"Sample1", "metadata":null},
{"id":"Sample2", "metadata":null},
{"id":"Sample3", "metadata":null},
{"id":"Sample4", "metadata":null},
{"id":"Sample5", "metadata":null},
{"id":"Sample6", "metadata":null}
],
"matrix_type": "sparse",
"matrix_element_type": "int",
"shape": [5, 6],
"data":[[0,2,1],
[1,0,5],
[1,1,1],
[1,3,2],
[1,4,3],
[1,5,1],
[2,2,1],
[2,3,4],
[2,5,2],
[3,0,2],
[3,1,1],
[3,2,1],
[3,5,1],
[4,1,1],
[4,2,1]
]
}"""
rich_dense_otu = """{
"id":null,
"format": "1.0.0",
"format_url": "http://biom-format.org",
"type": "OTU table",
"generated_by": "QIIME revision XYZ",
"date": "2011-12-19T19:00:00",
"rows":[{"id":"GG_OTU_1",
"metadata":{"taxonomy":["k__Bacteria",
"p__Proteobacteria",
"c__Gammaproteobacteria",
"o__Enterobacteriales",
"f__Enterobacteriaceae",
"g__Escherichia",
"s__"]}},
{"id":"GG_OTU_2",
"metadata":{"taxonomy":["k__Bacteria",
"p__Cyanobacteria",
"c__Nostocophycideae",
"o__Nostocales",
"f__Nostocaceae",
"g__Dolichospermum",
"s__"]}},
{"id":"GG_OTU_3",
"metadata":{"taxonomy":["k__Archaea",
"p__Euryarchaeota",
"c__Methanomicrobia",
"o__Methanosarcinales",
"f__Methanosarcinaceae",
"g__Methanosarcina",
"s__"]}},
{"id":"GG_OTU_4",
"metadata":{"taxonomy":["k__Bacteria",
"p__Firmicutes",
"c__Clostridia",
"o__Halanaerobiales",
"f__Halanaerobiaceae",
"g__Halanaerobium",
"s__Halanaerobiumsaccharolyticum"]}},
{"id":"GG_OTU_5",
"metadata":{"taxonomy":["k__Bacteria",
"p__Proteobacteria",
"c__Gammaproteobacteria",
"o__Enterobacteriales",
"f__Enterobacteriaceae",
"g__Escherichia",
"s__"]}}
],
"columns":[
{"id":"Sample1", "metadata":{
"BarcodeSequence":"CGCTTATCGAGA",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"gut",
"Description":"human gut"}},
{"id":"Sample2", "metadata":{
"BarcodeSequence":"CATACCAGTAGC",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"gut",
"Description":"human gut"}},
{"id":"Sample3", "metadata":{
"BarcodeSequence":"CTCTCTACCTGT",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"gut",
"Description":"human gut"}},
{"id":"Sample4", "metadata":{
"BarcodeSequence":"CTCTCGGCCTGT",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"skin",
"Description":"human skin"}},
{"id":"Sample5", "metadata":{
"BarcodeSequence":"CTCTCTACCAAT",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"skin",
"Description":"human skin"}},
{"id":"Sample6", "metadata":{
"BarcodeSequence":"CTAACTACCAAT",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"skin",
"Description":"human skin"}}
],
"matrix_type": "dense",
"matrix_element_type": "int",
"shape": [5,6],
"data": [[0,0,1,0,0,0],
[5,1,0,2,3,1],
[0,0,1,4,2,0],
[2,1,1,0,0,1],
[0,1,1,0,0,0]]
}"""
min_dense_otu = """ {
"id":null,
"format": "1.0.0",
"format_url": "http://biom-format.org",
"type": "OTU table",
"generated_by": "QIIME revision XYZ",
"date": "2011-12-19T19:00:00",
"rows":[
{"id":"GG_OTU_1", "metadata":null},
{"id":"GG_OTU_2", "metadata":null},
{"id":"GG_OTU_3", "metadata":null},
{"id":"GG_OTU_4", "metadata":null},
{"id":"GG_OTU_5", "metadata":null}
],
"columns": [
{"id":"Sample1", "metadata":null},
{"id":"Sample2", "metadata":null},
{"id":"Sample3", "metadata":null},
{"id":"Sample4", "metadata":null},
{"id":"Sample5", "metadata":null},
{"id":"Sample6", "metadata":null}
],
"matrix_type": "dense",
"matrix_element_type": "int",
"shape": [5,6],
"data": [[0,0,1,0,0,0],
[5,1,0,2,3,1],
[0,0,1,4,2,0],
[2,1,1,0,0,1],
[0,1,1,0,0,0]]
}"""
if __name__ == "__main__":
main()
|
