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
|
%global _empty_manifest_terminate_build 0
Name: python-BactInspectorMax
Version: 0.1.3
Release: 1
Summary: Package to investigate mash hits against refseq
License: MIT
URL: https://pypi.org/project/BactInspectorMax/
Source0: https://mirrors.aliyun.com/pypi/web/packages/97/e3/087fb0be0414f1442d01e481e0ad22e8596680c98e6462b8513cbe307ee9/BactInspectorMax-0.1.3.tar.gz
BuildArch: noarch
Requires: python3-pandas
Requires: python3-numpy
%description
# Bactinspector
A package to
1. determine the most probable species based on sequence in fasta/fastq files using refseq and Mash (https://mash.readthedocs.io/en/latest/index.html)
It will count the species of the top ref seq mash matches and report most frequent.
2. determine the closest reference in refseq to a set of fasta/fastq files
The PyPi package is called BactInspectorMax since my original BactInspector asked for the path to a sketch
of refseq genomes. In May 2019 a new curated mash sketch of complete bacterial refseq genome was
created and bundled into the package. This required a special request to increase the PyPi package limit,
hence the Max.
The command is still `bactinspector <sub command>` however.
## Data
The data bundled into bactinspector are the complete bacterial refseq genomes from May 2019. The species assignations have been corrected by changing species where the majority does not match the species described within the refseq info found [here](ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt) and the excellent [Bacsort resource](https://github.com/rrwick/Bacsort) from [Ryan Wick](https://twitter.com/rrwick)
## Dependencies
[Mash](https://github.com/marbl/Mash/) (> v2.1)
Installation with conda is recommended
## Installation
pip3 install bactinspectorMax
## Usage
```
usage: bactinspector [-h] [-v]
{check_species,closest_match,info,create_species_info} ...
A module to determine the most probable species based on sequence in fasta files using refseq and Mash (https://mash.readthedocs.io/en/latest/index.html)
It will count the species of the top ref seq mash matches and report most frequent.
In order to use the module:
• Specify an input directory and output directory (default is current directory)
• Specify either a
• fasta file pattern with -f (e.g "*.fas") or
• mash sketch file pattern with -m (e.g "*.msh") if you have already sketched the fasta files
• By default the top 10 matches will be used. Change this with -n
• Speed things up by changing the number of parallel processes to match the cores on your computer using -p
• If mash is not in your PATH specify the directory containing the mash executable with -mp
If you want to update the genomes used, follow the instructions on https://gitlab.com/antunderwood/bactinspector/wikis/Updating-the-genomes-in-BactInspector
and use the create_species_info command to make the required file
positional arguments:
{check_species,closest_match,create_species_info}
The following commands are available. Type
bactinspector <COMMAND> -h for more help on a specific
commands
check_species Check the most frequent matches to a species in refseq
closest_match Report the closest matches to a set of sequences
create_species_info
Create species info TSV for locally created mash
sketches
info Provide information about the data in bactinspector
optional arguments:
-h, --help show this help message and exit
-v, --version print out software version
```
### check_species
Assign a species using matches to refseq. Based on observed intra-species mash distances, a result maybe marked as uncertain if the distance to the best hit is greater than 1.2 x the observed maximum intra-species distance.
```
usage: bactinspector check_species [-h] [-i INPUT_DIR] [-o OUTPUT_DIR]
[-p PARALLEL_PROCESSES]
[-n NUM_BEST_MATCHES] [-d DISTANCE_CUTOFF]
[-v ALLOWED_VARIANCE]
[-vl ALLOWED_VARIANCE_RARER_SPECIES] [-s]
[-l LOCAL_MASH_AND_INFO_FILE_PREFIX]
[-mp MASH_PATH]
(-f FASTA_FILE_PATTERN | -fq FASTQ_FILE_PATTERN | -m MASH_SKETCH_FILE_PATTERN)
optional arguments:
-h, --help show this help message and exit
-i INPUT_DIR, --input_dir INPUT_DIR
path to input_directory
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
path to output_directory
-p PARALLEL_PROCESSES, --parallel_processes PARALLEL_PROCESSES
number of processes to run in parallel
-n NUM_BEST_MATCHES, --num_best_matches NUM_BEST_MATCHES
number of best matches to return
-d DISTANCE_CUTOFF, --distance_cutoff DISTANCE_CUTOFF
mash distance cutoff (default 0.05)
-v ALLOWED_VARIANCE, --allowed_variance ALLOWED_VARIANCE
proportion of max_distance allowed over which a result
will be marked as uncertain (default 0.1)
-vl ALLOWED_VARIANCE_RARER_SPECIES, --allowed_variance_rarer_species ALLOWED_VARIANCE_RARER_SPECIES
proportion of max_distance allowed over which a result
will be marked as uncertain for species which have
fewer than 10 representatives in refseq (default 0.5)
-s, --stdout_summary output a summary of the result to STDOUT
-l LOCAL_MASH_AND_INFO_FILE_PREFIX, --local_mash_and_info_file_prefix LOCAL_MASH_AND_INFO_FILE_PREFIX
the path prefix to the mash sketch file and
corresponding info file
-mp MASH_PATH, --mash_path MASH_PATH
path to the mash executable. If not provided it is
assumed mash is in the PATH
-f FASTA_FILE_PATTERN, --fasta_file_pattern FASTA_FILE_PATTERN
pattern to match fasta files e.g "*.fas"
-fq FASTQ_FILE_PATTERN, --fastq_file_pattern FASTQ_FILE_PATTERN
pattern to match fastq files e.g "*.fastq.gz"
-m MASH_SKETCH_FILE_PATTERN, --mash_sketch_file_pattern MASH_SKETCH_FILE_PATTERN
pattern to match mash sketch files e.g "*.msh"
```
### closest_match
Find the closest match of a set of genomes to genomes within refseq. Useful as an objective way of choosing a reference genome when mapping
```
usage: bactinspector closest_match [-h] [-i INPUT_DIR] [-o OUTPUT_DIR]
[-p PARALLEL_PROCESSES] [-r]
[-l LOCAL_MASH_AND_INFO_FILE_PREFIX]
[-mp MASH_PATH]
(-f FASTA_FILE_PATTERN | -fq FASTQ_FILE_PATTERN | -m MASH_SKETCH_FILE_PATTERN)
optional arguments:
-h, --help show this help message and exit
-i INPUT_DIR, --input_dir INPUT_DIR
path to input_directory
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
path to output_directory
-p PARALLEL_PROCESSES, --parallel_processes PARALLEL_PROCESSES
number of processes to run in parallel
-r, --ref_and_rep_only
only include reference and representative sequences
-l LOCAL_MASH_AND_INFO_FILE_PREFIX, --local_mash_and_info_file_prefix LOCAL_MASH_AND_INFO_FILE_PREFIX
the path prefix to the mash sketch file and
corresponding info file
-mp MASH_PATH, --mash_path MASH_PATH
path to the mash executable. If not provided it is
assumed mash is in the PATH
-f FASTA_FILE_PATTERN, --fasta_file_pattern FASTA_FILE_PATTERN
pattern to match fasta files e.g "*.fas"
-fq FASTQ_FILE_PATTERN, --fastq_file_pattern FASTQ_FILE_PATTERN
pattern to match fastq files e.g "*.fastq.gz"
-m MASH_SKETCH_FILE_PATTERN, --mash_sketch_file_pattern MASH_SKETCH_FILE_PATTERN
pattern to match mash sketch files e.g "*.msh"
```
### info
Find out what sequences are present in the mash sketch using a term to search the species name. You can either specify `-s` to search the aggregated species information or `-i` to search the individual refseq records.
```
usage: bactinspector info [-h] -t SEARCH_TERM (-s | -i)
optional arguments:
-h, --help show this help message and exit
-t SEARCH_TERM, --search_term SEARCH_TERM
search term to use when searching species within
bactinspector
-s, --summary search the aggregate data
-i, --individual_records
search the individual refseq records
```
### create_species_info
An updated mash sketch file and corresponding info file can be created using the process described [here](https://gitlab.com/antunderwood/bactinspector/wikis/Updating-the-genomes-in-BactInspector)
This process uses the create_species_info commmand
```
usage: bactinspector create_species_info [-h] -m MASH_INFO_FILE -r
REFSEQ_SUMMARY_FILE -b
BACSORT_SPECIES_FILE -x
BACSORT_EXCLUDED_ASSEMBLIES_FILE
optional arguments:
-h, --help show this help message and exit
-m MASH_INFO_FILE, --mash_info_file MASH_INFO_FILE
path to info file created using mash info -t
-r REFSEQ_SUMMARY_FILE, --refseq_summary_file REFSEQ_SUMMARY_FILE
path to refseq assembly summary file downloaded via
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteri
a/assembly_summary.txt
-b BACSORT_SPECIES_FILE, --bacsort_species_file BACSORT_SPECIES_FILE
path to bacsort_species_definitions.txt
-x BACSORT_EXCLUDED_ASSEMBLIES_FILE, --bacsort_excluded_assemblies_file BACSORT_EXCLUDED_ASSEMBLIES_FILE
path to bacsort_excluded_assemblies.txt
```
%package -n python3-BactInspectorMax
Summary: Package to investigate mash hits against refseq
Provides: python-BactInspectorMax
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-BactInspectorMax
# Bactinspector
A package to
1. determine the most probable species based on sequence in fasta/fastq files using refseq and Mash (https://mash.readthedocs.io/en/latest/index.html)
It will count the species of the top ref seq mash matches and report most frequent.
2. determine the closest reference in refseq to a set of fasta/fastq files
The PyPi package is called BactInspectorMax since my original BactInspector asked for the path to a sketch
of refseq genomes. In May 2019 a new curated mash sketch of complete bacterial refseq genome was
created and bundled into the package. This required a special request to increase the PyPi package limit,
hence the Max.
The command is still `bactinspector <sub command>` however.
## Data
The data bundled into bactinspector are the complete bacterial refseq genomes from May 2019. The species assignations have been corrected by changing species where the majority does not match the species described within the refseq info found [here](ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt) and the excellent [Bacsort resource](https://github.com/rrwick/Bacsort) from [Ryan Wick](https://twitter.com/rrwick)
## Dependencies
[Mash](https://github.com/marbl/Mash/) (> v2.1)
Installation with conda is recommended
## Installation
pip3 install bactinspectorMax
## Usage
```
usage: bactinspector [-h] [-v]
{check_species,closest_match,info,create_species_info} ...
A module to determine the most probable species based on sequence in fasta files using refseq and Mash (https://mash.readthedocs.io/en/latest/index.html)
It will count the species of the top ref seq mash matches and report most frequent.
In order to use the module:
• Specify an input directory and output directory (default is current directory)
• Specify either a
• fasta file pattern with -f (e.g "*.fas") or
• mash sketch file pattern with -m (e.g "*.msh") if you have already sketched the fasta files
• By default the top 10 matches will be used. Change this with -n
• Speed things up by changing the number of parallel processes to match the cores on your computer using -p
• If mash is not in your PATH specify the directory containing the mash executable with -mp
If you want to update the genomes used, follow the instructions on https://gitlab.com/antunderwood/bactinspector/wikis/Updating-the-genomes-in-BactInspector
and use the create_species_info command to make the required file
positional arguments:
{check_species,closest_match,create_species_info}
The following commands are available. Type
bactinspector <COMMAND> -h for more help on a specific
commands
check_species Check the most frequent matches to a species in refseq
closest_match Report the closest matches to a set of sequences
create_species_info
Create species info TSV for locally created mash
sketches
info Provide information about the data in bactinspector
optional arguments:
-h, --help show this help message and exit
-v, --version print out software version
```
### check_species
Assign a species using matches to refseq. Based on observed intra-species mash distances, a result maybe marked as uncertain if the distance to the best hit is greater than 1.2 x the observed maximum intra-species distance.
```
usage: bactinspector check_species [-h] [-i INPUT_DIR] [-o OUTPUT_DIR]
[-p PARALLEL_PROCESSES]
[-n NUM_BEST_MATCHES] [-d DISTANCE_CUTOFF]
[-v ALLOWED_VARIANCE]
[-vl ALLOWED_VARIANCE_RARER_SPECIES] [-s]
[-l LOCAL_MASH_AND_INFO_FILE_PREFIX]
[-mp MASH_PATH]
(-f FASTA_FILE_PATTERN | -fq FASTQ_FILE_PATTERN | -m MASH_SKETCH_FILE_PATTERN)
optional arguments:
-h, --help show this help message and exit
-i INPUT_DIR, --input_dir INPUT_DIR
path to input_directory
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
path to output_directory
-p PARALLEL_PROCESSES, --parallel_processes PARALLEL_PROCESSES
number of processes to run in parallel
-n NUM_BEST_MATCHES, --num_best_matches NUM_BEST_MATCHES
number of best matches to return
-d DISTANCE_CUTOFF, --distance_cutoff DISTANCE_CUTOFF
mash distance cutoff (default 0.05)
-v ALLOWED_VARIANCE, --allowed_variance ALLOWED_VARIANCE
proportion of max_distance allowed over which a result
will be marked as uncertain (default 0.1)
-vl ALLOWED_VARIANCE_RARER_SPECIES, --allowed_variance_rarer_species ALLOWED_VARIANCE_RARER_SPECIES
proportion of max_distance allowed over which a result
will be marked as uncertain for species which have
fewer than 10 representatives in refseq (default 0.5)
-s, --stdout_summary output a summary of the result to STDOUT
-l LOCAL_MASH_AND_INFO_FILE_PREFIX, --local_mash_and_info_file_prefix LOCAL_MASH_AND_INFO_FILE_PREFIX
the path prefix to the mash sketch file and
corresponding info file
-mp MASH_PATH, --mash_path MASH_PATH
path to the mash executable. If not provided it is
assumed mash is in the PATH
-f FASTA_FILE_PATTERN, --fasta_file_pattern FASTA_FILE_PATTERN
pattern to match fasta files e.g "*.fas"
-fq FASTQ_FILE_PATTERN, --fastq_file_pattern FASTQ_FILE_PATTERN
pattern to match fastq files e.g "*.fastq.gz"
-m MASH_SKETCH_FILE_PATTERN, --mash_sketch_file_pattern MASH_SKETCH_FILE_PATTERN
pattern to match mash sketch files e.g "*.msh"
```
### closest_match
Find the closest match of a set of genomes to genomes within refseq. Useful as an objective way of choosing a reference genome when mapping
```
usage: bactinspector closest_match [-h] [-i INPUT_DIR] [-o OUTPUT_DIR]
[-p PARALLEL_PROCESSES] [-r]
[-l LOCAL_MASH_AND_INFO_FILE_PREFIX]
[-mp MASH_PATH]
(-f FASTA_FILE_PATTERN | -fq FASTQ_FILE_PATTERN | -m MASH_SKETCH_FILE_PATTERN)
optional arguments:
-h, --help show this help message and exit
-i INPUT_DIR, --input_dir INPUT_DIR
path to input_directory
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
path to output_directory
-p PARALLEL_PROCESSES, --parallel_processes PARALLEL_PROCESSES
number of processes to run in parallel
-r, --ref_and_rep_only
only include reference and representative sequences
-l LOCAL_MASH_AND_INFO_FILE_PREFIX, --local_mash_and_info_file_prefix LOCAL_MASH_AND_INFO_FILE_PREFIX
the path prefix to the mash sketch file and
corresponding info file
-mp MASH_PATH, --mash_path MASH_PATH
path to the mash executable. If not provided it is
assumed mash is in the PATH
-f FASTA_FILE_PATTERN, --fasta_file_pattern FASTA_FILE_PATTERN
pattern to match fasta files e.g "*.fas"
-fq FASTQ_FILE_PATTERN, --fastq_file_pattern FASTQ_FILE_PATTERN
pattern to match fastq files e.g "*.fastq.gz"
-m MASH_SKETCH_FILE_PATTERN, --mash_sketch_file_pattern MASH_SKETCH_FILE_PATTERN
pattern to match mash sketch files e.g "*.msh"
```
### info
Find out what sequences are present in the mash sketch using a term to search the species name. You can either specify `-s` to search the aggregated species information or `-i` to search the individual refseq records.
```
usage: bactinspector info [-h] -t SEARCH_TERM (-s | -i)
optional arguments:
-h, --help show this help message and exit
-t SEARCH_TERM, --search_term SEARCH_TERM
search term to use when searching species within
bactinspector
-s, --summary search the aggregate data
-i, --individual_records
search the individual refseq records
```
### create_species_info
An updated mash sketch file and corresponding info file can be created using the process described [here](https://gitlab.com/antunderwood/bactinspector/wikis/Updating-the-genomes-in-BactInspector)
This process uses the create_species_info commmand
```
usage: bactinspector create_species_info [-h] -m MASH_INFO_FILE -r
REFSEQ_SUMMARY_FILE -b
BACSORT_SPECIES_FILE -x
BACSORT_EXCLUDED_ASSEMBLIES_FILE
optional arguments:
-h, --help show this help message and exit
-m MASH_INFO_FILE, --mash_info_file MASH_INFO_FILE
path to info file created using mash info -t
-r REFSEQ_SUMMARY_FILE, --refseq_summary_file REFSEQ_SUMMARY_FILE
path to refseq assembly summary file downloaded via
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteri
a/assembly_summary.txt
-b BACSORT_SPECIES_FILE, --bacsort_species_file BACSORT_SPECIES_FILE
path to bacsort_species_definitions.txt
-x BACSORT_EXCLUDED_ASSEMBLIES_FILE, --bacsort_excluded_assemblies_file BACSORT_EXCLUDED_ASSEMBLIES_FILE
path to bacsort_excluded_assemblies.txt
```
%package help
Summary: Development documents and examples for BactInspectorMax
Provides: python3-BactInspectorMax-doc
%description help
# Bactinspector
A package to
1. determine the most probable species based on sequence in fasta/fastq files using refseq and Mash (https://mash.readthedocs.io/en/latest/index.html)
It will count the species of the top ref seq mash matches and report most frequent.
2. determine the closest reference in refseq to a set of fasta/fastq files
The PyPi package is called BactInspectorMax since my original BactInspector asked for the path to a sketch
of refseq genomes. In May 2019 a new curated mash sketch of complete bacterial refseq genome was
created and bundled into the package. This required a special request to increase the PyPi package limit,
hence the Max.
The command is still `bactinspector <sub command>` however.
## Data
The data bundled into bactinspector are the complete bacterial refseq genomes from May 2019. The species assignations have been corrected by changing species where the majority does not match the species described within the refseq info found [here](ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt) and the excellent [Bacsort resource](https://github.com/rrwick/Bacsort) from [Ryan Wick](https://twitter.com/rrwick)
## Dependencies
[Mash](https://github.com/marbl/Mash/) (> v2.1)
Installation with conda is recommended
## Installation
pip3 install bactinspectorMax
## Usage
```
usage: bactinspector [-h] [-v]
{check_species,closest_match,info,create_species_info} ...
A module to determine the most probable species based on sequence in fasta files using refseq and Mash (https://mash.readthedocs.io/en/latest/index.html)
It will count the species of the top ref seq mash matches and report most frequent.
In order to use the module:
• Specify an input directory and output directory (default is current directory)
• Specify either a
• fasta file pattern with -f (e.g "*.fas") or
• mash sketch file pattern with -m (e.g "*.msh") if you have already sketched the fasta files
• By default the top 10 matches will be used. Change this with -n
• Speed things up by changing the number of parallel processes to match the cores on your computer using -p
• If mash is not in your PATH specify the directory containing the mash executable with -mp
If you want to update the genomes used, follow the instructions on https://gitlab.com/antunderwood/bactinspector/wikis/Updating-the-genomes-in-BactInspector
and use the create_species_info command to make the required file
positional arguments:
{check_species,closest_match,create_species_info}
The following commands are available. Type
bactinspector <COMMAND> -h for more help on a specific
commands
check_species Check the most frequent matches to a species in refseq
closest_match Report the closest matches to a set of sequences
create_species_info
Create species info TSV for locally created mash
sketches
info Provide information about the data in bactinspector
optional arguments:
-h, --help show this help message and exit
-v, --version print out software version
```
### check_species
Assign a species using matches to refseq. Based on observed intra-species mash distances, a result maybe marked as uncertain if the distance to the best hit is greater than 1.2 x the observed maximum intra-species distance.
```
usage: bactinspector check_species [-h] [-i INPUT_DIR] [-o OUTPUT_DIR]
[-p PARALLEL_PROCESSES]
[-n NUM_BEST_MATCHES] [-d DISTANCE_CUTOFF]
[-v ALLOWED_VARIANCE]
[-vl ALLOWED_VARIANCE_RARER_SPECIES] [-s]
[-l LOCAL_MASH_AND_INFO_FILE_PREFIX]
[-mp MASH_PATH]
(-f FASTA_FILE_PATTERN | -fq FASTQ_FILE_PATTERN | -m MASH_SKETCH_FILE_PATTERN)
optional arguments:
-h, --help show this help message and exit
-i INPUT_DIR, --input_dir INPUT_DIR
path to input_directory
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
path to output_directory
-p PARALLEL_PROCESSES, --parallel_processes PARALLEL_PROCESSES
number of processes to run in parallel
-n NUM_BEST_MATCHES, --num_best_matches NUM_BEST_MATCHES
number of best matches to return
-d DISTANCE_CUTOFF, --distance_cutoff DISTANCE_CUTOFF
mash distance cutoff (default 0.05)
-v ALLOWED_VARIANCE, --allowed_variance ALLOWED_VARIANCE
proportion of max_distance allowed over which a result
will be marked as uncertain (default 0.1)
-vl ALLOWED_VARIANCE_RARER_SPECIES, --allowed_variance_rarer_species ALLOWED_VARIANCE_RARER_SPECIES
proportion of max_distance allowed over which a result
will be marked as uncertain for species which have
fewer than 10 representatives in refseq (default 0.5)
-s, --stdout_summary output a summary of the result to STDOUT
-l LOCAL_MASH_AND_INFO_FILE_PREFIX, --local_mash_and_info_file_prefix LOCAL_MASH_AND_INFO_FILE_PREFIX
the path prefix to the mash sketch file and
corresponding info file
-mp MASH_PATH, --mash_path MASH_PATH
path to the mash executable. If not provided it is
assumed mash is in the PATH
-f FASTA_FILE_PATTERN, --fasta_file_pattern FASTA_FILE_PATTERN
pattern to match fasta files e.g "*.fas"
-fq FASTQ_FILE_PATTERN, --fastq_file_pattern FASTQ_FILE_PATTERN
pattern to match fastq files e.g "*.fastq.gz"
-m MASH_SKETCH_FILE_PATTERN, --mash_sketch_file_pattern MASH_SKETCH_FILE_PATTERN
pattern to match mash sketch files e.g "*.msh"
```
### closest_match
Find the closest match of a set of genomes to genomes within refseq. Useful as an objective way of choosing a reference genome when mapping
```
usage: bactinspector closest_match [-h] [-i INPUT_DIR] [-o OUTPUT_DIR]
[-p PARALLEL_PROCESSES] [-r]
[-l LOCAL_MASH_AND_INFO_FILE_PREFIX]
[-mp MASH_PATH]
(-f FASTA_FILE_PATTERN | -fq FASTQ_FILE_PATTERN | -m MASH_SKETCH_FILE_PATTERN)
optional arguments:
-h, --help show this help message and exit
-i INPUT_DIR, --input_dir INPUT_DIR
path to input_directory
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
path to output_directory
-p PARALLEL_PROCESSES, --parallel_processes PARALLEL_PROCESSES
number of processes to run in parallel
-r, --ref_and_rep_only
only include reference and representative sequences
-l LOCAL_MASH_AND_INFO_FILE_PREFIX, --local_mash_and_info_file_prefix LOCAL_MASH_AND_INFO_FILE_PREFIX
the path prefix to the mash sketch file and
corresponding info file
-mp MASH_PATH, --mash_path MASH_PATH
path to the mash executable. If not provided it is
assumed mash is in the PATH
-f FASTA_FILE_PATTERN, --fasta_file_pattern FASTA_FILE_PATTERN
pattern to match fasta files e.g "*.fas"
-fq FASTQ_FILE_PATTERN, --fastq_file_pattern FASTQ_FILE_PATTERN
pattern to match fastq files e.g "*.fastq.gz"
-m MASH_SKETCH_FILE_PATTERN, --mash_sketch_file_pattern MASH_SKETCH_FILE_PATTERN
pattern to match mash sketch files e.g "*.msh"
```
### info
Find out what sequences are present in the mash sketch using a term to search the species name. You can either specify `-s` to search the aggregated species information or `-i` to search the individual refseq records.
```
usage: bactinspector info [-h] -t SEARCH_TERM (-s | -i)
optional arguments:
-h, --help show this help message and exit
-t SEARCH_TERM, --search_term SEARCH_TERM
search term to use when searching species within
bactinspector
-s, --summary search the aggregate data
-i, --individual_records
search the individual refseq records
```
### create_species_info
An updated mash sketch file and corresponding info file can be created using the process described [here](https://gitlab.com/antunderwood/bactinspector/wikis/Updating-the-genomes-in-BactInspector)
This process uses the create_species_info commmand
```
usage: bactinspector create_species_info [-h] -m MASH_INFO_FILE -r
REFSEQ_SUMMARY_FILE -b
BACSORT_SPECIES_FILE -x
BACSORT_EXCLUDED_ASSEMBLIES_FILE
optional arguments:
-h, --help show this help message and exit
-m MASH_INFO_FILE, --mash_info_file MASH_INFO_FILE
path to info file created using mash info -t
-r REFSEQ_SUMMARY_FILE, --refseq_summary_file REFSEQ_SUMMARY_FILE
path to refseq assembly summary file downloaded via
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteri
a/assembly_summary.txt
-b BACSORT_SPECIES_FILE, --bacsort_species_file BACSORT_SPECIES_FILE
path to bacsort_species_definitions.txt
-x BACSORT_EXCLUDED_ASSEMBLIES_FILE, --bacsort_excluded_assemblies_file BACSORT_EXCLUDED_ASSEMBLIES_FILE
path to bacsort_excluded_assemblies.txt
```
%prep
%autosetup -n BactInspectorMax-0.1.3
%build
%py3_build
%install
%py3_install
install -d -m755 %{buildroot}/%{_pkgdocdir}
if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
pushd %{buildroot}
if [ -d usr/lib ]; then
find usr/lib -type f -printf "\"/%h/%f\"\n" >> filelist.lst
fi
if [ -d usr/lib64 ]; then
find usr/lib64 -type f -printf "\"/%h/%f\"\n" >> filelist.lst
fi
if [ -d usr/bin ]; then
find usr/bin -type f -printf "\"/%h/%f\"\n" >> filelist.lst
fi
if [ -d usr/sbin ]; then
find usr/sbin -type f -printf "\"/%h/%f\"\n" >> filelist.lst
fi
touch doclist.lst
if [ -d usr/share/man ]; then
find usr/share/man -type f -printf "\"/%h/%f.gz\"\n" >> doclist.lst
fi
popd
mv %{buildroot}/filelist.lst .
mv %{buildroot}/doclist.lst .
%files -n python3-BactInspectorMax -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Thu Jun 08 2023 Python_Bot <Python_Bot@openeuler.org> - 0.1.3-1
- Package Spec generated
|
