Mercurial > repos > iss > eurl_vtec_wgs_pt
comparison scripts/patho_typing.py @ 0:c6bab5103a14 draft
"planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"
author | iss |
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date | Mon, 21 Mar 2022 15:23:09 +0000 |
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1 #!/usr/bin/env python3 | |
2 | |
3 # -*- coding: utf-8 -*- | |
4 | |
5 """ | |
6 patho_typing.py - In silico pathogenic typing directly from raw | |
7 Illumina reads | |
8 <https://github.com/B-UMMI/patho_typing/> | |
9 | |
10 Copyright (C) 2018 Miguel Machado <mpmachado@medicina.ulisboa.pt> | |
11 | |
12 Last modified: October 15, 2018 | |
13 | |
14 This program is free software: you can redistribute it and/or modify | |
15 it under the terms of the GNU General Public License as published by | |
16 the Free Software Foundation, either version 3 of the License, or | |
17 (at your option) any later version. | |
18 | |
19 This program is distributed in the hope that it will be useful, | |
20 but WITHOUT ANY WARRANTY; without even the implied warranty of | |
21 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
22 GNU General Public License for more details. | |
23 | |
24 You should have received a copy of the GNU General Public License | |
25 along with this program. If not, see <http://www.gnu.org/licenses/>. | |
26 | |
27 2020-01-13 ISS | |
28 In order to use the module within the EURL_WGS_Typer pipeline with a | |
29 different virulence database for E coli, mapping against the | |
30 typing_rules.tab was deactivated. | |
31 """ | |
32 | |
33 import argparse | |
34 import os | |
35 import time | |
36 import sys | |
37 from pkg_resources import resource_filename | |
38 | |
39 try: | |
40 from __init__ import __version__ | |
41 | |
42 import modules.utils as utils | |
43 import modules.run_rematch as run_rematch | |
44 import modules.typing as typing | |
45 except ImportError: | |
46 from pathotyping.__init__ import __version__ | |
47 | |
48 from pathotyping.modules import utils as utils | |
49 from pathotyping.modules import run_rematch as run_rematch | |
50 from pathotyping.modules import typing as typing | |
51 | |
52 | |
53 def set_reference(species, outdir, script_path, trueCoverage): | |
54 reference_file = None | |
55 trueCoverage_file = None | |
56 trueCoverage_sequences = None | |
57 trueCoverage_headers = None | |
58 trueCoverage_config = None | |
59 typing_file = None | |
60 typing_sequences = None | |
61 typing_headers = None | |
62 typing_rules = None | |
63 typing_config = None | |
64 | |
65 species_folder = os.path.join(os.path.dirname(script_path), 'modules', 'seq_conf', | |
66 '_'.join([s.lower() for s in species]), '') | |
67 | |
68 if os.path.isdir(species_folder): | |
69 typing_rules = os.path.join(species_folder, 'typing_rules.tab') | |
70 typing_file = os.path.join(species_folder, 'typing.fasta') | |
71 typing_sequences, ignore = utils.get_sequence_information(typing_file, 0) | |
72 typing_sequences, typing_headers = utils.clean_headers_sequences(typing_sequences) | |
73 typing_sequences = utils.simplify_sequence_dict(typing_sequences) | |
74 typing_config = os.path.join(species_folder, 'typing.config') | |
75 if trueCoverage: | |
76 if os.path.isfile(os.path.join(species_folder, 'trueCoverage.fasta')): | |
77 trueCoverage_file = os.path.join(species_folder, 'trueCoverage.fasta') | |
78 trueCoverage_sequences, ignore = utils.get_sequence_information(trueCoverage_file, 0) | |
79 trueCoverage_sequences, trueCoverage_headers = utils.clean_headers_sequences(trueCoverage_sequences) | |
80 trueCoverage_sequences = utils.simplify_sequence_dict(trueCoverage_sequences) | |
81 trueCoverage_config = os.path.join(species_folder, 'trueCoverage.config') | |
82 | |
83 trueCoverage_typing_sequences = trueCoverage_sequences.copy() | |
84 for header in typing_sequences: | |
85 if header not in trueCoverage_sequences: | |
86 trueCoverage_typing_sequences[header] = typing_sequences[header] | |
87 else: | |
88 print('Sequence {header} of typing.fasta already present in' | |
89 ' trueCoverage.fasta'.format(header=header)) | |
90 | |
91 reference_file = os.path.join(outdir, 'trueCoverage_typing.fasta') | |
92 write_sequeces(reference_file, trueCoverage_typing_sequences) | |
93 else: | |
94 reference_file = os.path.join(outdir, 'typing.fasta') | |
95 write_sequeces(reference_file, typing_sequences) | |
96 else: | |
97 species_present = [] | |
98 seq_conf_folder = os.path.join(os.path.dirname(script_path), 'modules', 'seq_conf', '') | |
99 species_folder = [d for d in os.listdir(seq_conf_folder) if | |
100 not d.startswith('.') and os.path.isdir(os.path.join(seq_conf_folder, d, ''))] | |
101 for species in species_folder: | |
102 species = species.split('_') | |
103 species[0] = species[0][0].upper() + species[0][1:] | |
104 species_present.append(' '.join(species)) | |
105 sys.exit('Only these species are available:' + '\n' + '\n'.join(species_present)) | |
106 | |
107 return reference_file, trueCoverage_file, trueCoverage_sequences, trueCoverage_headers, trueCoverage_config, \ | |
108 typing_file, typing_sequences, typing_headers, typing_rules, typing_config | |
109 | |
110 | |
111 def index_fasta_samtools(fasta, region_None, region_outfile_none, print_comand_True): | |
112 command = ['samtools', 'faidx', fasta, '', '', ''] | |
113 shell_true = False | |
114 if region_None is not None: | |
115 command[3] = region_None | |
116 if region_outfile_none is not None: | |
117 command[4] = '>' | |
118 command[5] = region_outfile_none | |
119 shell_true = True | |
120 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, shell_true, None, print_comand_True) | |
121 return run_successfully, stdout | |
122 | |
123 | |
124 def indexSequenceBowtie2(referenceFile, threads): | |
125 if os.path.isfile(str(referenceFile + '.1.bt2')): | |
126 run_successfully = True | |
127 else: | |
128 command = ['bowtie2-build', '--threads', str(threads), referenceFile, referenceFile] | |
129 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True) | |
130 return run_successfully | |
131 | |
132 | |
133 def run_bowtie(fastq_files, referenceFile, threads, outdir, conserved_True, numMapLoc): | |
134 sam_file = os.path.join(outdir, str('alignment.sam')) | |
135 | |
136 run_successfully = indexSequenceBowtie2(referenceFile, threads) | |
137 if run_successfully: | |
138 command = ['bowtie2', '-k', str(numMapLoc), '-q', '', '--threads', str(threads), '-x', referenceFile, '', | |
139 '--no-unal', '-S', sam_file] | |
140 | |
141 if len(fastq_files) == 1: | |
142 command[9] = '-U ' + fastq_files[0] | |
143 elif len(fastq_files) == 2: | |
144 command[9] = '-1 ' + fastq_files[0] + ' -2 ' + fastq_files[1] | |
145 else: | |
146 return False, None | |
147 | |
148 if conserved_True: | |
149 command[4] = '--sensitive' | |
150 else: | |
151 command[4] = '--very-sensitive-local' | |
152 | |
153 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True) | |
154 | |
155 if not run_successfully: | |
156 sam_file = None | |
157 | |
158 return run_successfully, sam_file | |
159 | |
160 | |
161 def sortAlignment(alignment_file, output_file, sortByName_True, threads): | |
162 outFormat_string = os.path.splitext(output_file)[1][1:].lower() | |
163 command = ['samtools', 'sort', '-o', output_file, '-O', outFormat_string, '', '-@', str(threads), alignment_file] | |
164 if sortByName_True: | |
165 command[6] = '-n' | |
166 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True) | |
167 if not run_successfully: | |
168 output_file = None | |
169 return run_successfully, output_file | |
170 | |
171 | |
172 def indexAlignment(alignment_file): | |
173 command = ['samtools', 'index', alignment_file] | |
174 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True) | |
175 return run_successfully | |
176 | |
177 | |
178 def mapping_reads(fastq_files, referenceFile, threads, outdir, conserved_True, numMapLoc): | |
179 print('\n' + 'Mapping the reads' + '\n') | |
180 run_successfully, sam_file = run_bowtie(fastq_files, referenceFile, threads, outdir, conserved_True, numMapLoc) | |
181 bam_file = None | |
182 if run_successfully: | |
183 run_successfully, bam_file = sortAlignment(sam_file, str(os.path.splitext(sam_file)[0] + '.bam'), False, | |
184 threads) | |
185 if run_successfully: | |
186 os.remove(sam_file) | |
187 run_successfully = indexAlignment(bam_file) | |
188 if run_successfully: | |
189 index_fasta_samtools(referenceFile, None, None, True) | |
190 return run_successfully, bam_file | |
191 | |
192 | |
193 def include_rematch_dependencies_path(): | |
194 original_rematch = None | |
195 command = ['which', 'rematch.py'] | |
196 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, False) | |
197 if run_successfully: | |
198 original_rematch = stdout.splitlines()[0] | |
199 | |
200 resource_rematch = None | |
201 try: | |
202 resource_rematch = resource_filename('ReMatCh', 'rematch.py') | |
203 except ModuleNotFoundError: | |
204 resource_rematch = original_rematch | |
205 else: | |
206 print('\n' | |
207 'Using ReMatCh "{resource_rematch}" via "{original_rematch}"\n'.format(resource_rematch=resource_rematch, | |
208 original_rematch=original_rematch)) | |
209 | |
210 if resource_rematch is not None: | |
211 utils.setPATHvariable(False, resource_rematch) | |
212 else: | |
213 sys.exit('ReMatCh not found in the PATH') | |
214 | |
215 return resource_rematch | |
216 | |
217 | |
218 def split_bam(bam_file, list_sequences, outdir, threads): | |
219 new_bam = os.path.join(outdir, 'partial.bam') | |
220 command = ['samtools', 'view', '-b', '-u', '-h', '-o', new_bam, '-@', str(threads), bam_file, | |
221 ' '.join(list_sequences)] | |
222 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True) | |
223 return run_successfully, new_bam | |
224 | |
225 | |
226 def parse_config(config_file): | |
227 config = {'reference_file': None, 'length_extra_seq': None, 'maximum_number_absent_genes': None, | |
228 'maximum_number_genes_multiple_alleles': None, 'minimum_read_coverage': None, | |
229 'minimum_depth_presence': None, 'minimum_depth_call': None, | |
230 'minimum_depth_frequency_dominant_allele': None, 'minimum_gene_coverage': None, | |
231 'minimum_gene_identity': None} | |
232 | |
233 with open(config_file, 'rt') as reader: | |
234 field = None | |
235 for line in reader: | |
236 line = line.splitlines()[0] | |
237 if len(line) > 0: | |
238 line = line.split(' ')[0] | |
239 if line.startswith('#'): | |
240 line = line[1:].split(' ')[0] | |
241 field = line | |
242 else: | |
243 if field is not None: | |
244 if field in ['length_extra_seq', 'maximum_number_absent_genes', | |
245 'maximum_number_genes_multiple_alleles', 'minimum_read_coverage', | |
246 'minimum_depth_presence', 'minimum_depth_call', 'minimum_gene_coverage', | |
247 'minimum_gene_identity']: | |
248 line = int(line) | |
249 if field in ['minimum_gene_coverage', 'minimum_gene_identity']: | |
250 if line < 0 or line > 100: | |
251 sys.exit('minimum_gene_coverage in trueCoverage_rematch config file must be an' | |
252 ' integer between 0 and 100') | |
253 elif field == 'minimum_depth_frequency_dominant_allele': | |
254 line = float(line) | |
255 if line < 0 or line > 1: | |
256 sys.exit('minimum_depth_frequency_dominant_allele in trueCoverage_rematch config file' | |
257 ' must be a double between 0 and 1') | |
258 config[field] = line | |
259 field = None | |
260 | |
261 for field in config: | |
262 if config[field] is None: | |
263 sys.exit(field + ' in trueCoverage_rematch config file is missing') | |
264 | |
265 return config | |
266 | |
267 | |
268 def clean_pathotyping_folder(outdir, reference_file, debug_mode_true): | |
269 if not debug_mode_true: | |
270 files = [f for f in os.listdir(outdir) if not f.startswith('.') and os.path.isfile(os.path.join(outdir, f))] | |
271 for file_found in files: | |
272 if file_found.startswith(('alignment.', os.path.splitext(os.path.basename(reference_file))[0])): | |
273 file_found = os.path.join(outdir, file_found) | |
274 os.remove(file_found) | |
275 | |
276 | |
277 def write_sequeces(out_file, sequences_dict): | |
278 with open(out_file, 'wt') as writer: | |
279 for header in sequences_dict: | |
280 writer.write('>' + header + '\n') | |
281 writer.write('\n'.join(utils.chunkstring(sequences_dict[header]['sequence'], 80)) + '\n') | |
282 | |
283 | |
284 def main(): | |
285 parser = argparse.ArgumentParser(prog='patho_typing.py', | |
286 description='In silico pathogenic typing directly from raw Illumina reads', | |
287 formatter_class=argparse.ArgumentDefaultsHelpFormatter) | |
288 parser.add_argument('--version', help='Version information', action='version', | |
289 version='{prog} v{version}'.format(prog=parser.prog, version=__version__)) | |
290 | |
291 parser_required = parser.add_argument_group('Required options') | |
292 parser_required.add_argument('-f', '--fastq', nargs='+', action=utils.required_length((1, 2), '--fastq'), | |
293 type=argparse.FileType('r'), metavar=('/path/to/input/file.fq.gz'), | |
294 help='Path to single OR paired-end fastq files. If two files are passed, they will be' | |
295 ' assumed as being the paired fastq files', required=True) | |
296 parser_required.add_argument('-s', '--species', nargs=2, type=str, metavar=('Yersinia', 'enterocolitica'), | |
297 help='Species name', required=True) | |
298 | |
299 parser_optional_general = parser.add_argument_group('General facultative options') | |
300 parser_optional_general.add_argument('-o', '--outdir', type=str, metavar='/path/to/output/directory/', | |
301 help='Path to the directory where the information will be stored', | |
302 required=False, default='.') | |
303 parser_optional_general.add_argument('-j', '--threads', type=int, metavar='N', help='Number of threads to use', | |
304 required=False, default=1) | |
305 parser_optional_general.add_argument('--trueCoverage', action='store_true', | |
306 help='Assess true coverage before continue typing') | |
307 parser_optional_general.add_argument('--noCheckPoint', action='store_true', | |
308 help='Ignore the true coverage checking point') | |
309 parser_optional_general.add_argument('--minGeneCoverage', type=int, metavar='N', | |
310 help='Minimum typing percentage of target reference gene sequence covered to' | |
311 ' consider a gene to be present (value between [0, 100])', required=False) | |
312 parser_optional_general.add_argument('--minGeneIdentity', type=int, metavar='N', | |
313 help='Minimum typing percentage of identity of reference gene sequence covered' | |
314 ' to consider a gene to be present (value between [0, 100]). One INDEL' | |
315 ' will be considered as one difference', required=False) | |
316 parser_optional_general.add_argument('--minGeneDepth', type=int, metavar='N', | |
317 help='Minimum typing gene average coverage depth of present positions to' | |
318 ' consider a gene to be present (default is 1/3 of average sample' | |
319 ' coverage or 15x)', required=False) | |
320 parser_optional_general.add_argument('--doNotRemoveConsensus', action='store_true', | |
321 help='Do not remove ReMatCh consensus sequences') | |
322 parser_optional_general.add_argument('--debug', action='store_true', | |
323 help='DeBug Mode: do not remove temporary files') | |
324 | |
325 args = parser.parse_args() | |
326 | |
327 if args.minGeneCoverage is not None and (args.minGeneCoverage < 0 or args.minGeneCoverage > 100): | |
328 parser.error('--minGeneCoverage should be a value between [0, 100]') | |
329 if args.minGeneIdentity is not None and (args.minGeneIdentity < 0 or args.minGeneIdentity > 100): | |
330 parser.error('--minGeneIdentity should be a value between [0, 100]') | |
331 | |
332 start_time = time.time() | |
333 | |
334 args.outdir = os.path.abspath(args.outdir) | |
335 if not os.path.isdir(args.outdir): | |
336 os.makedirs(args.outdir) | |
337 | |
338 # Start logger | |
339 logfile, time_str = utils.start_logger(args.outdir) | |
340 | |
341 script_path = utils.general_information(logfile, __version__, args.outdir, time_str) | |
342 print('\n') | |
343 | |
344 rematch = include_rematch_dependencies_path() | |
345 | |
346 args.fastq = [fastq.name for fastq in args.fastq] | |
347 | |
348 reference_file, trueCoverage_file, trueCoverage_sequences, trueCoverage_headers, trueCoverage_config, typing_file, \ | |
349 typing_sequences, typing_headers, typing_rules, typing_config = \ | |
350 set_reference(args.species, args.outdir, script_path, args.trueCoverage) | |
351 original_reference_file = str(reference_file) | |
352 | |
353 run_successfully, bam_file = mapping_reads(args.fastq, reference_file, args.threads, args.outdir, False, 1) | |
354 if run_successfully: | |
355 rematch_dir = os.path.join(args.outdir, 'rematch', '') | |
356 if not os.path.isdir(rematch_dir): | |
357 os.makedirs(rematch_dir) | |
358 | |
359 if args.trueCoverage: | |
360 if trueCoverage_file is not None: | |
361 trueCoverage_dir = os.path.join(rematch_dir, 'trueCoverage', '') | |
362 if not os.path.isdir(trueCoverage_dir): | |
363 os.makedirs(trueCoverage_dir) | |
364 | |
365 print('\n') | |
366 run_successfully, trueCoverage_bam = split_bam(bam_file, trueCoverage_headers, trueCoverage_dir, | |
367 args.threads) | |
368 if run_successfully: | |
369 run_successfully = indexAlignment(trueCoverage_bam) | |
370 if run_successfully: | |
371 reference_file = os.path.join(trueCoverage_dir, 'reference.fasta') | |
372 write_sequeces(reference_file, trueCoverage_sequences) | |
373 index_fasta_samtools(reference_file, None, None, True) | |
374 config = parse_config(trueCoverage_config) | |
375 runtime, run_successfully, sample_data_general, data_by_gene = \ | |
376 run_rematch.run_rematch(rematch, trueCoverage_dir, reference_file, trueCoverage_bam, | |
377 args.threads, config['length_extra_seq'], | |
378 config['minimum_depth_presence'], config['minimum_depth_call'], | |
379 config['minimum_depth_frequency_dominant_allele'], | |
380 config['minimum_gene_coverage'], config['minimum_gene_identity'], | |
381 args.debug, args.doNotRemoveConsensus) | |
382 | |
383 if run_successfully and sample_data_general['mean_sample_coverage'] is not None and \ | |
384 sample_data_general['number_absent_genes'] is not None and \ | |
385 sample_data_general['number_genes_multiple_alleles'] is not None: | |
386 if args.minGeneDepth is None: | |
387 args.minGeneDepth = sample_data_general['mean_sample_coverage'] / 3 if \ | |
388 sample_data_general['mean_sample_coverage'] / 3 > 15 else \ | |
389 15 | |
390 | |
391 exit_info = [] | |
392 if sample_data_general['mean_sample_coverage'] < config['minimum_read_coverage']: | |
393 exit_info.append('Sample coverage ({mean}) lower than the minimum' | |
394 ' required ({minimum})' | |
395 ''.format(mean=sample_data_general['mean_sample_coverage'], | |
396 minimum=config['minimum_read_coverage'])) | |
397 if sample_data_general['number_absent_genes'] > config['maximum_number_absent_genes']: | |
398 exit_info.append('Number of absent genes ({number}) higher than the' | |
399 ' maximum allowed ({maximum})' | |
400 ''.format(number=sample_data_general['number_absent_genes'], | |
401 maximum=config['maximum_number_absent_genes'])) | |
402 if sample_data_general['number_genes_multiple_alleles'] > \ | |
403 config['maximum_number_genes_multiple_alleles']: | |
404 exit_info.append('Number of genes with multiple alleles' | |
405 ' ({number}) higher than the maximum' | |
406 ' allowed ({maximum})' | |
407 ''.format(number=sample_data_general['number_genes_multiple_alleles'], | |
408 maximum=config['maximum_number_genes_multiple_alleles'])) | |
409 | |
410 if len(exit_info) > 0: | |
411 print('\n' + '\n'.join(exit_info) + '\n') | |
412 e = 'TrueCoverage requirements not fulfilled' | |
413 print('\n' + e + '\n') | |
414 if not args.noCheckPoint: | |
415 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug) | |
416 _ = utils.runTime(start_time) | |
417 sys.exit(e) | |
418 else: | |
419 e = 'TrueCoverage module did not run successfully' | |
420 print('\n' + e + '\n') | |
421 if not args.noCheckPoint: | |
422 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug) | |
423 _ = utils.runTime(start_time) | |
424 sys.exit(e) | |
425 | |
426 print('\n') | |
427 typing_dir = os.path.join(rematch_dir, 'typing', '') | |
428 if not os.path.isdir(typing_dir): | |
429 os.makedirs(typing_dir) | |
430 run_successfully, bam_file = split_bam(bam_file, typing_headers, typing_dir, args.threads) | |
431 if run_successfully: | |
432 run_successfully = indexAlignment(bam_file) | |
433 if run_successfully: | |
434 reference_file = os.path.join(typing_dir, 'reference.fasta') | |
435 write_sequeces(reference_file, typing_sequences) | |
436 index_fasta_samtools(reference_file, None, None, True) | |
437 rematch_dir = str(typing_dir) | |
438 if not run_successfully: | |
439 if args.noCheckPoint: | |
440 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug) | |
441 _ = utils.runTime(start_time) | |
442 sys.exit('Something in the required TrueCoverage analysis went wrong') | |
443 else: | |
444 print('\n' | |
445 'WARNING: it was not found trueCoverage target files. trueCoverage will not run.' | |
446 '\n') | |
447 | |
448 if run_successfully: | |
449 config = parse_config(typing_config) | |
450 if args.minGeneCoverage is not None: | |
451 config['minimum_gene_coverage'] = args.minGeneCoverage | |
452 if args.minGeneIdentity is not None: | |
453 config['minimum_gene_identity'] = args.minGeneIdentity | |
454 | |
455 runtime, run_successfully, sample_data_general, data_by_gene = \ | |
456 run_rematch.run_rematch(rematch, rematch_dir, reference_file, bam_file, args.threads, | |
457 config['length_extra_seq'], config['minimum_depth_presence'], | |
458 config['minimum_depth_call'], config['minimum_depth_frequency_dominant_allele'], | |
459 config['minimum_gene_coverage'], config['minimum_gene_identity'], | |
460 args.debug, args.doNotRemoveConsensus) | |
461 if run_successfully and data_by_gene is not None: | |
462 if args.minGeneDepth is None: | |
463 args.minGeneDepth = sample_data_general['mean_sample_coverage'] / 3 if \ | |
464 sample_data_general['mean_sample_coverage'] / 3 > 15 else \ | |
465 15 | |
466 else: | |
467 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug) | |
468 _ = utils.runTime(start_time) | |
469 sys.exit('ReMatCh run for pathotyping did not run successfully') | |
470 else: | |
471 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug) | |
472 _ = utils.runTime(start_time) | |
473 sys.exit('Something did not run successfully') | |
474 | |
475 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug) | |
476 | |
477 print('\n') | |
478 _ = utils.runTime(start_time) | |
479 | |
480 | |
481 if __name__ == "__main__": | |
482 main() |