comparison pima_report.py @ 14:95b1d1a9497d draft

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author greg
date Fri, 17 Mar 2023 17:23:43 +0000
parents f03c80bb22e9
children 02283aa193c3
comparison
equal deleted inserted replaced
13:f03c80bb22e9 14:95b1d1a9497d
7 import sys 7 import sys
8 8
9 from Bio import SeqIO 9 from Bio import SeqIO
10 from datetime import date 10 from datetime import date
11 from mdutils.mdutils import MdUtils 11 from mdutils.mdutils import MdUtils
12 # FIXME: TableOfContents doesn't work.
13 # from mdutils.tools import TableOfContents
12 14
13 CDC_ADVISORY = 'The analysis and report presented here should be treated as preliminary. Please contact the CDC/BDRD with any results regarding _Bacillus anthracis_.' 15 CDC_ADVISORY = 'The analysis and report presented here should be treated as preliminary. Please contact the CDC/BDRD with any results regarding _Bacillus anthracis_.'
14 16
15 17
16 class PimaReport: 18 class PimaReport:
17 19
18 def __init__(self, analysis_name=None, amr_deletions_file=None, amr_matrix_files=None, assembly_fasta_file=None, 20 def __init__(self, analysis_name=None, amr_deletions_file=None, amr_matrix_files=None, assembly_fasta_file=None,
19 assembly_name=None, bedtools_version=None, blastn_version=None, circos_files=None, 21 assembly_name=None, bedtools_version=None, blastn_version=None, circos_files=None,
20 compute_sequence_length_file=None, contig_coverage_file=None, dbkey=None, dnadiff_snps_file=None, 22 compute_sequence_length_file=None, contig_coverage_file=None, dbkey=None, dnadiff_snps_file=None,
21 dnadiff_version=None, feature_bed_files=None, feature_png_files=None, flye_assembly_info_file=None, 23 dnadiff_version=None, feature_bed_files=None, feature_png_files=None, flye_assembly_info_file=None,
22 flye_version=None, genome_insertions_file=None, gzipped=None, illumina_fastq_file=None, 24 flye_version=None, genome_insertions_file=None, gzipped=None, kraken2_report_file=None,
23 kraken2_report_file=None, kraken2_version=None, minimap2_version=None, mutation_regions_bed_file=None, 25 kraken2_version=None, minimap2_version=None, mutation_regions_bed_file=None, mutation_regions_tsv_files=None,
24 mutation_regions_tsv_files=None, pima_css=None, plasmids_file=None, quast_report_file=None, 26 ont_fastq_file=None, pima_css=None, plasmids_file=None, quast_report_file=None, reference_insertions_file=None,
25 reference_insertions_file=None, samtools_version=None, varscan_version=None): 27 samtools_version=None, varscan_version=None):
26 self.ofh = open("process_log.txt", "w") 28 self.ofh = open("process_log.txt", "w")
27 29
28 self.ofh.write("amr_deletions_file: %s\n" % str(amr_deletions_file)) 30 self.ofh.write("amr_deletions_file: %s\n" % str(amr_deletions_file))
29 self.ofh.write("amr_matrix_files: %s\n" % str(amr_matrix_files)) 31 self.ofh.write("amr_matrix_files: %s\n" % str(amr_matrix_files))
30 self.ofh.write("analysis_name: %s\n" % str(analysis_name)) 32 self.ofh.write("analysis_name: %s\n" % str(analysis_name))
42 self.ofh.write("feature_png_files: %s\n" % str(feature_png_files)) 44 self.ofh.write("feature_png_files: %s\n" % str(feature_png_files))
43 self.ofh.write("flye_assembly_info_file: %s\n" % str(flye_assembly_info_file)) 45 self.ofh.write("flye_assembly_info_file: %s\n" % str(flye_assembly_info_file))
44 self.ofh.write("flye_version: %s\n" % str(flye_version)) 46 self.ofh.write("flye_version: %s\n" % str(flye_version))
45 self.ofh.write("gzipped: %s\n" % str(gzipped)) 47 self.ofh.write("gzipped: %s\n" % str(gzipped))
46 self.ofh.write("genome_insertions_file: %s\n" % str(genome_insertions_file)) 48 self.ofh.write("genome_insertions_file: %s\n" % str(genome_insertions_file))
47 self.ofh.write("illumina_fastq_file: %s\n" % str(illumina_fastq_file))
48 self.ofh.write("kraken2_report_file: %s\n" % str(kraken2_report_file)) 49 self.ofh.write("kraken2_report_file: %s\n" % str(kraken2_report_file))
49 self.ofh.write("kraken2_version: %s\n" % str(kraken2_version)) 50 self.ofh.write("kraken2_version: %s\n" % str(kraken2_version))
50 self.ofh.write("minimap2_version: %s\n" % str(minimap2_version)) 51 self.ofh.write("minimap2_version: %s\n" % str(minimap2_version))
51 self.ofh.write("mutation_regions_bed_file: %s\n" % str(mutation_regions_bed_file)) 52 self.ofh.write("mutation_regions_bed_file: %s\n" % str(mutation_regions_bed_file))
52 self.ofh.write("mutation_regions_tsv_files: %s\n" % str(mutation_regions_tsv_files)) 53 self.ofh.write("mutation_regions_tsv_files: %s\n" % str(mutation_regions_tsv_files))
54 self.ofh.write("ont_fastq_file: %s\n" % str(ont_fastq_file))
53 self.ofh.write("pima_css: %s\n" % str(pima_css)) 55 self.ofh.write("pima_css: %s\n" % str(pima_css))
54 self.ofh.write("plasmids_file: %s\n" % str(plasmids_file)) 56 self.ofh.write("plasmids_file: %s\n" % str(plasmids_file))
55 self.ofh.write("quast_report_file: %s\n" % str(quast_report_file)) 57 self.ofh.write("quast_report_file: %s\n" % str(quast_report_file))
56 self.ofh.write("reference_insertions_file: %s\n" % str(reference_insertions_file)) 58 self.ofh.write("reference_insertions_file: %s\n" % str(reference_insertions_file))
57 self.ofh.write("samtools_version: %s\n" % str(samtools_version)) 59 self.ofh.write("samtools_version: %s\n" % str(samtools_version))
92 self.flye_version = 'flye (version unknown)' 94 self.flye_version = 'flye (version unknown)'
93 else: 95 else:
94 self.flye_version = re.sub('_', '.', flye_version.rstrip(' _assembly info_')) 96 self.flye_version = re.sub('_', '.', flye_version.rstrip(' _assembly info_'))
95 self.gzipped = gzipped 97 self.gzipped = gzipped
96 self.genome_insertions_file = genome_insertions_file 98 self.genome_insertions_file = genome_insertions_file
97 self.illumina_fastq_file = illumina_fastq_file
98 self.kraken2_report_file = kraken2_report_file 99 self.kraken2_report_file = kraken2_report_file
99 if kraken2_version is None: 100 if kraken2_version is None:
100 self.kraken2_version = 'kraken2 (version unknown)' 101 self.kraken2_version = 'kraken2 (version unknown)'
101 else: 102 else:
102 self.kraken2_version = re.sub('_', '.', kraken2_version.rstrip(' _report_')) 103 self.kraken2_version = re.sub('_', '.', kraken2_version.rstrip(' _report_'))
104 self.minimap2_version = 'minimap2 (version unknown)' 105 self.minimap2_version = 'minimap2 (version unknown)'
105 else: 106 else:
106 self.minimap2_version = re.sub('_', '.', minimap2_version) 107 self.minimap2_version = re.sub('_', '.', minimap2_version)
107 self.mutation_regions_bed_file = mutation_regions_bed_file 108 self.mutation_regions_bed_file = mutation_regions_bed_file
108 self.mutation_regions_tsv_files = mutation_regions_tsv_files 109 self.mutation_regions_tsv_files = mutation_regions_tsv_files
109 self.read_type = 'Illumina'
110 self.ont_bases = None
111 self.ont_n50 = None
112 self.ont_read_count = None
113 self.pima_css = pima_css 110 self.pima_css = pima_css
114 self.plasmids_file = plasmids_file 111 self.plasmids_file = plasmids_file
115 self.quast_report_file = quast_report_file 112 self.quast_report_file = quast_report_file
113 self.read_type = 'ONT'
116 self.reference_insertions_file = reference_insertions_file 114 self.reference_insertions_file = reference_insertions_file
117 self.reference_insertions_file = reference_insertions_file 115 self.reference_insertions_file = reference_insertions_file
118 if samtools_version is None: 116 if samtools_version is None:
119 self.samtools_version = 'samtools (version unknown)' 117 self.samtools_version = 'samtools (version unknown)'
120 else: 118 else:
164 # Values 162 # Values
165 self.assembly_size = 0 163 self.assembly_size = 0
166 self.contig_info = None 164 self.contig_info = None
167 self.did_medaka_ont_assembly = False 165 self.did_medaka_ont_assembly = False
168 self.feature_hits = pandas.Series(dtype='float64') 166 self.feature_hits = pandas.Series(dtype='float64')
169 self.illumina_length_mean = 0 167 self.illumina_fastq_file = None
170 self.illumina_read_count = 0 168 self.illumina_length_mean = None
171 self.illumina_bases = 0 169 self.illumina_read_count = None
172 # TODO: should the following 2 values be passed as parameters? 170 self.illumina_bases = None
171 self.ont_bases = None
172 # TODO: should the following be passed as a parameter?
173 self.ont_coverage_min = 30
174 self.ont_fast5 = None
175 self.ont_fastq_file = ont_fastq_file
176 self.ont_n50 = None
177 # TODO: should the following be passed as a parameter?
173 self.ont_n50_min = 2500 178 self.ont_n50_min = 2500
174 self.ont_coverage_min = 30 179 self.ont_raw_fastq = self.analysis_name
180 self.ont_read_count = None
175 181
176 # Actions 182 # Actions
177 self.did_guppy_ont_fast5 = False 183 self.did_guppy_ont_fast5 = False
178 self.did_qcat_ont_fastq = False 184 self.did_qcat_ont_fastq = False
185 self.info_ont_fastq(self.ont_fastq_file)
179 self.info_illumina_fastq() 186 self.info_illumina_fastq()
180 self.load_contig_info() 187 self.load_contig_info()
181 188
182 def run_command(self, command): 189 def run_command(self, command):
183 self.ofh.write("\nXXXXXX In run_command, command:\n%s\n\n" % str(command)) 190 self.ofh.write("\nXXXXXX In run_command, command:\n%s\n\n" % str(command))
235 self.assembly_size += len(i.seq) 242 self.assembly_size += len(i.seq)
236 self.assembly_size = self.format_kmg(self.assembly_size, decimals=1) 243 self.assembly_size = self.format_kmg(self.assembly_size, decimals=1)
237 244
238 def info_illumina_fastq(self): 245 def info_illumina_fastq(self):
239 self.ofh.write("\nXXXXXX In info_illumina_fastq\n\n") 246 self.ofh.write("\nXXXXXX In info_illumina_fastq\n\n")
247 if self.illumina_length_mean is None:
248 return
240 if self.gzipped: 249 if self.gzipped:
241 opener = 'gunzip -c' 250 opener = 'gunzip -c'
242 else: 251 else:
243 opener = 'cat' 252 opener = 'cat'
244 command = ' '.join([opener, 253 command = ' '.join([opener,
245 self.illumina_fastq_file, 254 self.ont_fastq_file,
246 '| awk \'{getline;s += length($1);getline;getline;}END{print s/(NR/4)"\t"(NR/4)"\t"s}\'']) 255 '| awk \'{getline;s += length($1);getline;getline;}END{print s/(NR/4)"\t"(NR/4)"\t"s}\''])
247 output = self.run_command(command) 256 output = self.run_command(command)
248 self.ofh.write("output:\n%s\n" % str(output)) 257 self.ofh.write("output:\n%s\n" % str(output))
249 self.ofh.write("re.split('\\t', self.run_command(command)[0]:\n%s\n" % str(re.split('\\t', self.run_command(command)[0]))) 258 self.ofh.write("re.split('\\t', self.run_command(command)[0]:\n%s\n" % str(re.split('\\t', self.run_command(command)[0])))
250 values = [] 259 values = []
258 self.illumina_length_mean += values[0] 267 self.illumina_length_mean += values[0]
259 self.ofh.write("values[1]:\n%s\n" % str(values[1])) 268 self.ofh.write("values[1]:\n%s\n" % str(values[1]))
260 self.illumina_read_count += int(values[1]) 269 self.illumina_read_count += int(values[1])
261 self.ofh.write("values[2]:\n%s\n" % str(values[2])) 270 self.ofh.write("values[2]:\n%s\n" % str(values[2]))
262 self.illumina_bases += int(values[2]) 271 self.illumina_bases += int(values[2])
263 # The original PIMA code inserts self.illumina_fastq into 272 # The original PIMA code inserts self.illumina_fastq_file into
264 # a list for no apparent reason. We don't do that here. 273 # a list for no apparent reason. We don't do that here.
265 # self.illumina_length_mean /= len(self.illumina_fastq) 274 # self.illumina_length_mean /= len(self.illumina_fastq_file)
266 self.illumina_length_mean /= 1 275 self.illumina_length_mean /= 1
267 self.illumina_bases = self.format_kmg(self.illumina_bases, decimals=1) 276 self.illumina_bases = self.format_kmg(self.illumina_bases, decimals=1)
268 277
269 def start_doc(self): 278 def start_doc(self):
270 header_text = 'Analysis of ' + self.analysis_name 279 header_text = 'Analysis of ' + self.analysis_name
271 self.doc = MdUtils(file_name=self.report_md, title=header_text) 280 self.doc = MdUtils(file_name=self.report_md, title=header_text)
281
282 def add_table_of_contents(self):
283 self.doc.create_marker(text_marker="TableOfContents")
284 self.doc.new_line()
285 self.doc.new_line('<div style="page-break-after: always;"></div>')
286 self.doc.new_line()
272 287
273 def add_run_information(self): 288 def add_run_information(self):
274 self.ofh.write("\nXXXXXX In add_run_information\n\n") 289 self.ofh.write("\nXXXXXX In add_run_information\n\n")
275 self.doc.new_line() 290 self.doc.new_line()
276 self.doc.new_header(1, 'Run information') 291 self.doc.new_header(1, 'Run information')
279 "Category", 294 "Category",
280 "Information", 295 "Information",
281 "Date", 296 "Date",
282 date.today(), 297 date.today(),
283 "ONT FAST5", 298 "ONT FAST5",
284 "N/A", 299 self.wordwrap_markdown(self.ont_fast5),
285 "ONT FASTQ", 300 "ONT FASTQ",
286 "N/A", 301 self.wordwrap_markdown(self.ont_raw_fastq),
287 "Illumina FASTQ", 302 "Illumina FASTQ",
288 self.wordwrap_markdown(self.analysis_name), 303 self.wordwrap_markdown(self.illumina_fastq_file),
289 "Assembly", 304 "Assembly",
290 self.wordwrap_markdown(self.assembly_name), 305 self.wordwrap_markdown(self.assembly_name),
291 "Reference", 306 "Reference",
292 self.wordwrap_markdown(self.dbkey), 307 self.wordwrap_markdown(self.dbkey),
293 ] 308 ]
294 self.doc.new_table(columns=2, rows=7, text=Table_list, text_align='left') 309 self.doc.new_table(columns=2, rows=7, text=Table_list, text_align='left')
295 self.doc.new_line() 310 self.doc.new_line()
311 # FIXME: the following doesn't work.
312 # self.add_table_of_contents()
296 self.doc.new_line() 313 self.doc.new_line()
297 314
298 def add_ont_library_information(self): 315 def add_ont_library_information(self):
299 self.ofh.write("\nXXXXXX In add_ont_library_information\n\n") 316 self.ofh.write("\nXXXXXX In add_ont_library_information\n\n")
300 if self.ont_n50 is None: 317 if self.ont_n50 is None:
309 "ONT reads", 326 "ONT reads",
310 '{:,}'.format(self.ont_read_count), 327 '{:,}'.format(self.ont_read_count),
311 "ONT bases", 328 "ONT bases",
312 '{:s}'.format(self.ont_bases), 329 '{:s}'.format(self.ont_bases),
313 "Illumina FASTQ", 330 "Illumina FASTQ",
314 self.wordwrap_markdown(self.illumina_fastq_file), 331 self.wordwrap_markdown(self.ont_fastq_file),
315 "Assembly", 332 "Assembly",
316 self.wordwrap_markdown(self.assembly_name), 333 self.wordwrap_markdown(self.assembly_name),
317 "Reference", 334 "Reference",
318 self.wordwrap_markdown(self.dbkey), 335 self.wordwrap_markdown(self.dbkey),
319 ] 336 ]
320 self.doc.new_table(columns=2, rows=7, text=Table_List, text_align='left') 337 self.doc.new_table(columns=2, rows=7, text=Table_List, text_align='left')
321 self.doc.new_line() 338 self.doc.new_line()
322 339
323 def add_illumina_library_information(self): 340 def add_illumina_library_information(self):
324 self.ofh.write("\nXXXXXX In add_illumina_library_information\n\n") 341 self.ofh.write("\nXXXXXX In add_illumina_library_information\n\n")
325 if self.illumina_length_mean == 0: 342 if self.illumina_length_mean is None:
326 return 343 return
327 self.doc.new_line() 344 self.doc.new_line()
328 self.doc.new_header(2, 'Illumina library statistics') 345 self.doc.new_header(2, 'Illumina library statistics')
329 Table_List = [ 346 Table_List = [
330 "Illumina Info.", 347 "Illumina Info.",
384 '{if(NR == 1){sub(/+/, "", $1);s=$1}else{bp += $1;if(bp > s / 2 && f == 0){n50 = $1;f = 1}}}', 401 '{if(NR == 1){sub(/+/, "", $1);s=$1}else{bp += $1;if(bp > s / 2 && f == 0){n50 = $1;f = 1}}}',
385 'END{printf "%d\\t%d\\t%d\\n", n50, (NR - 1), s;exit}\'']) 402 'END{printf "%d\\t%d\\t%d\\n", n50, (NR - 1), s;exit}\''])
386 result = list(re.split('\\t', self.run_command(command)[0])) 403 result = list(re.split('\\t', self.run_command(command)[0]))
387 if result[1] == '0': 404 if result[1] == '0':
388 self.error_out('No ONT reads found') 405 self.error_out('No ONT reads found')
389 ont_n50, ont_read_count, ont_raw_bases = [int(i) for i in result] 406 self.ont_n50, self.ont_read_count, ont_raw_bases = [int(i) for i in result]
390 command = ' '.join([opener, 407 command = ' '.join([opener,
391 fastq_file, 408 fastq_file,
392 '| awk \'{getline;print length($0);getline;getline;}\'']) 409 '| awk \'{getline;print length($0);getline;getline;}\''])
393 result = self.run_command(command) 410 result = self.run_command(command)
394 result = list(filter(lambda x: x != '', result)) 411 result = list(filter(lambda x: x != '', result))
395 # TODO: the following are not yet used... 412 self.ont_bases = self.format_kmg(ont_raw_bases, decimals=1)
396 # ont_read_lengths = [int(i) for i in result] 413 if self.ont_n50 <= self.ont_n50_min:
397 # ont_bases = self.format_kmg(ont_raw_bases, decimals=1) 414 warning = 'ONT N50 (%s) is less than the recommended minimum (%s)' % (str(self.ont_n50), str(self.ont_n50_min))
398 if ont_n50 <= self.ont_n50_min:
399 warning = 'ONT N50 (%s) is less than the recommended minimum (%s)' % (str(ont_n50), str(self.ont_n50_min))
400 self.assembly_notes = self.assembly_notes.append(pandas.Series(warning)) 415 self.assembly_notes = self.assembly_notes.append(pandas.Series(warning))
401 416
402 def wordwrap_markdown(self, string): 417 def wordwrap_markdown(self, string):
403 if string: 418 if string:
404 if len(string) < 35: 419 if len(string) < 35:
765 if self.did_guppy_ont_fast5: 780 if self.did_guppy_ont_fast5:
766 methods += ['ONT reads were basecalled using guppy'] 781 methods += ['ONT reads were basecalled using guppy']
767 if self.did_qcat_ont_fastq: 782 if self.did_qcat_ont_fastq:
768 methods += ['ONT reads were demultiplexed and trimmed using qcat'] 783 methods += ['ONT reads were demultiplexed and trimmed using qcat']
769 self.methods[self.basecalling_methods_title] = pandas.Series(methods) 784 self.methods[self.basecalling_methods_title] = pandas.Series(methods)
770 self.add_illumina_library_information() 785 # self.add_illumina_library_information()
771 self.add_contig_info() 786 self.add_contig_info()
772 self.evaluate_assembly() 787 self.evaluate_assembly()
773 self.add_assembly_information() 788 self.add_assembly_information()
774 if self.flye_assembly_info_file is not None: 789 if self.flye_assembly_info_file is not None:
775 method = 'ONT reads were assembled using %s' % self.flye_version.rstrip('assembly info') 790 method = 'ONT reads were assembled using %s' % self.flye_version.rstrip('assembly info')
783 warning = 'Flye reported {:d} open contigs ({:s}); assembly may be incomplete.'.format(open_contigs.shape[0], ', '.join(open_contig_ids)) 798 warning = 'Flye reported {:d} open contigs ({:s}); assembly may be incomplete.'.format(open_contigs.shape[0], ', '.join(open_contig_ids))
784 self.assembly_notes = self.assembly_notes.append(pandas.Series(warning)) 799 self.assembly_notes = self.assembly_notes.append(pandas.Series(warning))
785 if self.did_medaka_ont_assembly: 800 if self.did_medaka_ont_assembly:
786 method = 'the genome assembly was polished using ont reads and medaka.' 801 method = 'the genome assembly was polished using ont reads and medaka.'
787 self.methods[self.assembly_methods_title] = self.methods[self.assembly_methods_title].append(pandas.series(method)) 802 self.methods[self.assembly_methods_title] = self.methods[self.assembly_methods_title].append(pandas.series(method))
788 self.info_ont_fastq(self.illumina_fastq_file)
789 self.add_assembly_notes() 803 self.add_assembly_notes()
790 804
791 def make_tex(self): 805 def make_tex(self):
792 self.doc.new_table_of_contents(table_title='detailed run information', depth=2, marker="tableofcontents") 806 self.doc.new_table_of_contents(table_title='detailed run information', depth=2, marker="tableofcontents")
793 text = self.doc.file_data_text 807 text = self.doc.file_data_text
842 parser.add_argument('--feature_png_dir', action='store', dest='feature_png_dir', help='Directory of best feature hits png files') 856 parser.add_argument('--feature_png_dir', action='store', dest='feature_png_dir', help='Directory of best feature hits png files')
843 parser.add_argument('--flye_assembly_info_file', action='store', dest='flye_assembly_info_file', default=None, help='Flye assembly info tabular file') 857 parser.add_argument('--flye_assembly_info_file', action='store', dest='flye_assembly_info_file', default=None, help='Flye assembly info tabular file')
844 parser.add_argument('--flye_version', action='store', dest='flye_version', default=None, help='Flye version string') 858 parser.add_argument('--flye_version', action='store', dest='flye_version', default=None, help='Flye version string')
845 parser.add_argument('--genome_insertions_file', action='store', dest='genome_insertions_file', help='Genome insertions BED file') 859 parser.add_argument('--genome_insertions_file', action='store', dest='genome_insertions_file', help='Genome insertions BED file')
846 parser.add_argument('--gzipped', action='store_true', dest='gzipped', default=False, help='Input sample is gzipped') 860 parser.add_argument('--gzipped', action='store_true', dest='gzipped', default=False, help='Input sample is gzipped')
847 parser.add_argument('--illumina_fastq_file', action='store', dest='illumina_fastq_file', help='Input sample') 861 parser.add_argument('--ont_fastq_file', action='store', dest='ont_fastq_file', help='Input sample')
848 parser.add_argument('--kraken2_report_file', action='store', dest='kraken2_report_file', default=None, help='kraken2 report file') 862 parser.add_argument('--kraken2_report_file', action='store', dest='kraken2_report_file', default=None, help='kraken2 report file')
849 parser.add_argument('--kraken2_version', action='store', dest='kraken2_version', default=None, help='kraken2 version string') 863 parser.add_argument('--kraken2_version', action='store', dest='kraken2_version', default=None, help='kraken2 version string')
850 parser.add_argument('--minimap2_version', action='store', dest='minimap2_version', default=None, help='minimap2 version string') 864 parser.add_argument('--minimap2_version', action='store', dest='minimap2_version', default=None, help='minimap2 version string')
851 parser.add_argument('--mutation_regions_bed_file', action='store', dest='mutation_regions_bed_file', help='AMR mutation regions BRD file') 865 parser.add_argument('--mutation_regions_bed_file', action='store', dest='mutation_regions_bed_file', help='AMR mutation regions BRD file')
852 parser.add_argument('--mutation_regions_dir', action='store', dest='mutation_regions_dir', help='Directory of mutation regions TSV files') 866 parser.add_argument('--mutation_regions_dir', action='store', dest='mutation_regions_dir', help='Directory of mutation regions TSV files')
902 feature_png_files, 916 feature_png_files,
903 args.flye_assembly_info_file, 917 args.flye_assembly_info_file,
904 args.flye_version, 918 args.flye_version,
905 args.genome_insertions_file, 919 args.genome_insertions_file,
906 args.gzipped, 920 args.gzipped,
907 args.illumina_fastq_file,
908 args.kraken2_report_file, 921 args.kraken2_report_file,
909 args.kraken2_version, 922 args.kraken2_version,
910 args.minimap2_version, 923 args.minimap2_version,
911 args.mutation_regions_bed_file, 924 args.mutation_regions_bed_file,
912 mutation_regions_files, 925 mutation_regions_files,
926 args.ont_fastq_file,
913 args.pima_css, 927 args.pima_css,
914 args.plasmids_file, 928 args.plasmids_file,
915 args.quast_report_file, 929 args.quast_report_file,
916 args.reference_insertions_file, 930 args.reference_insertions_file,
917 args.samtools_version, 931 args.samtools_version,