Mercurial > repos > greg > pima_report

comparison pima_report.py @ 26:46edd7435555 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Tue, 25 Apr 2023 20:31:35 +0000
parents 4986a7fb2145
children ddc056cf16bf
comparison
equal deleted inserted replaced
25:4986a7fb2145 26:46edd7435555
18 class PimaReport: 18 class PimaReport:
19 19
20 def __init__(self, analysis_name=None, amr_deletions_file=None, amr_matrix_files=None, assembler_version=None, 20 def __init__(self, analysis_name=None, amr_deletions_file=None, amr_matrix_files=None, assembler_version=None,
21 assembly_fasta_file=None, assembly_name=None, bedtools_version=None, blastn_version=None, 21 assembly_fasta_file=None, assembly_name=None, bedtools_version=None, blastn_version=None,
22 circos_files=None, compute_sequence_length_file=None, contig_coverage_file=None, dbkey=None, 22 circos_files=None, compute_sequence_length_file=None, contig_coverage_file=None, dbkey=None,
23 dnadiff_snps_file=None, dnadiff_version=None, errors_file=None, fastq_file=None, feature_bed_files=None, 23 dnadiff_snps_file=None, dnadiff_version=None, errors_file=None, feature_bed_files=None,
24 feature_png_files=None, flye_assembly_info_file=None, genome_insertions_file=None, gzipped=None, 24 feature_png_files=None, flye_assembly_info_file=None, genome_insertions_file=None, gzipped=None,
25 kraken2_report_file=None, kraken2_version=None, minimap2_version=None, mutation_regions_bed_file=None, 25 illumina_forward_read_file=None, illumina_reverse_read_file=None, kraken2_report_file=None,
26 mutation_regions_tsv_files=None, pima_css=None, plasmids_file=None, quast_report_file=None, 26 kraken2_version=None, minimap2_version=None, mutation_regions_bed_file=None,
27 mutation_regions_tsv_files=None, ont_file=None, pima_css=None, plasmids_file=None, quast_report_file=None,
27 read_type=None, reference_insertions_file=None, samtools_version=None, varscan_version=None): 28 read_type=None, reference_insertions_file=None, samtools_version=None, varscan_version=None):
28 self.ofh = open("process_log.txt", "w") 29 self.ofh = open("process_log.txt", "w")
29 30
30 self.ofh.write("amr_deletions_file: %s\n" % str(amr_deletions_file)) 31 self.ofh.write("amr_deletions_file: %s\n" % str(amr_deletions_file))
31 self.ofh.write("amr_matrix_files: %s\n" % str(amr_matrix_files)) 32 self.ofh.write("amr_matrix_files: %s\n" % str(amr_matrix_files))
40 self.ofh.write("contig_coverage_file: %s\n" % str(contig_coverage_file)) 41 self.ofh.write("contig_coverage_file: %s\n" % str(contig_coverage_file))
41 self.ofh.write("dbkey: %s\n" % str(dbkey)) 42 self.ofh.write("dbkey: %s\n" % str(dbkey))
42 self.ofh.write("dnadiff_snps_file: %s\n" % str(dnadiff_snps_file)) 43 self.ofh.write("dnadiff_snps_file: %s\n" % str(dnadiff_snps_file))
43 self.ofh.write("dnadiff_version: %s\n" % str(dnadiff_version)) 44 self.ofh.write("dnadiff_version: %s\n" % str(dnadiff_version))
44 self.ofh.write("errors_file: %s\n" % str(errors_file)) 45 self.ofh.write("errors_file: %s\n" % str(errors_file))
45 self.ofh.write("fastq_file: %s\n" % str(fastq_file))
46 self.ofh.write("feature_bed_files: %s\n" % str(feature_bed_files)) 46 self.ofh.write("feature_bed_files: %s\n" % str(feature_bed_files))
47 self.ofh.write("feature_png_files: %s\n" % str(feature_png_files)) 47 self.ofh.write("feature_png_files: %s\n" % str(feature_png_files))
48 self.ofh.write("flye_assembly_info_file: %s\n" % str(flye_assembly_info_file)) 48 self.ofh.write("flye_assembly_info_file: %s\n" % str(flye_assembly_info_file))
49 self.ofh.write("gzipped: %s\n" % str(gzipped)) 49 self.ofh.write("gzipped: %s\n" % str(gzipped))
50 self.ofh.write("genome_insertions_file: %s\n" % str(genome_insertions_file)) 50 self.ofh.write("genome_insertions_file: %s\n" % str(genome_insertions_file))
51 self.ofh.write("illumina_forward_read_file: %s\n" % str(illumina_forward_read_file))
52 self.ofh.write("illumina_reverse_read_file: %s\n" % str(illumina_reverse_read_file))
51 self.ofh.write("kraken2_report_file: %s\n" % str(kraken2_report_file)) 53 self.ofh.write("kraken2_report_file: %s\n" % str(kraken2_report_file))
52 self.ofh.write("kraken2_version: %s\n" % str(kraken2_version)) 54 self.ofh.write("kraken2_version: %s\n" % str(kraken2_version))
53 self.ofh.write("minimap2_version: %s\n" % str(minimap2_version)) 55 self.ofh.write("minimap2_version: %s\n" % str(minimap2_version))
54 self.ofh.write("mutation_regions_bed_file: %s\n" % str(mutation_regions_bed_file)) 56 self.ofh.write("mutation_regions_bed_file: %s\n" % str(mutation_regions_bed_file))
55 self.ofh.write("mutation_regions_tsv_files: %s\n" % str(mutation_regions_tsv_files)) 57 self.ofh.write("mutation_regions_tsv_files: %s\n" % str(mutation_regions_tsv_files))
58 self.ofh.write("ont_file: %s\n" % str(ont_file))
56 self.ofh.write("pima_css: %s\n" % str(pima_css)) 59 self.ofh.write("pima_css: %s\n" % str(pima_css))
57 self.ofh.write("plasmids_file: %s\n" % str(plasmids_file)) 60 self.ofh.write("plasmids_file: %s\n" % str(plasmids_file))
58 self.ofh.write("quast_report_file: %s\n" % str(quast_report_file)) 61 self.ofh.write("quast_report_file: %s\n" % str(quast_report_file))
59 self.ofh.write("read_type: %s\n" % str(read_type)) 62 self.ofh.write("read_type: %s\n" % str(read_type))
60 self.ofh.write("reference_insertions_file: %s\n" % str(reference_insertions_file)) 63 self.ofh.write("reference_insertions_file: %s\n" % str(reference_insertions_file))
103 self.feature_bed_files = feature_bed_files 106 self.feature_bed_files = feature_bed_files
104 self.feature_png_files = feature_png_files 107 self.feature_png_files = feature_png_files
105 self.flye_assembly_info_file = flye_assembly_info_file 108 self.flye_assembly_info_file = flye_assembly_info_file
106 self.gzipped = gzipped 109 self.gzipped = gzipped
107 self.genome_insertions_file = genome_insertions_file 110 self.genome_insertions_file = genome_insertions_file
111 self.illumina_forward_read_file = illumina_forward_read_file
112 self.illumina_reverse_read_file = illumina_reverse_read_file
108 self.kraken2_report_file = kraken2_report_file 113 self.kraken2_report_file = kraken2_report_file
109 if kraken2_version is None: 114 if kraken2_version is None:
110 self.kraken2_version = 'kraken2 (version unknown)' 115 self.kraken2_version = 'kraken2 (version unknown)'
111 else: 116 else:
112 self.kraken2_version = re.sub('_', '.', kraken2_version.rstrip(' _report_')) 117 self.kraken2_version = re.sub('_', '.', kraken2_version.rstrip(' _report_'))
172 self.contig_alignment = pandas.Series(dtype=object) 177 self.contig_alignment = pandas.Series(dtype=object)
173 178
174 # Values 179 # Values
175 self.assembly_size = 0 180 self.assembly_size = 0
176 self.contig_info = None 181 self.contig_info = None
177 self.did_medaka_ont_assembly = False
178 self.feature_hits = pandas.Series(dtype='float64') 182 self.feature_hits = pandas.Series(dtype='float64')
179 self.illumina_length_mean = None 183 self.ont_fast5 = None
180 self.illumina_read_count = None 184 self.ont_file = ont_file
181 self.illumina_bases = None 185 self.ont_n50 = None
182 self.ont_bases = None 186 self.ont_read_count = None
183 # TODO: should the following be passed as a parameter? 187 # TODO: should the following be passed as a parameter?
184 self.ont_coverage_min = 30 188 self.ont_coverage_min = 30
185 self.ont_fast5 = None
186 self.fastq_file = fastq_file
187 self.ont_n50 = None
188 # TODO: should the following be passed as a parameter? 189 # TODO: should the following be passed as a parameter?
189 self.ont_n50_min = 2500 190 self.ont_n50_min = 2500
191
190 if self.read_type == 'ONT': 192 if self.read_type == 'ONT':
191 self.ont_raw_fastq = self.analysis_name 193 self.ont_raw_fastq = self.analysis_name
194 self.ont_bases = 0
195 self.illumina_bases = None
192 self.illumina_fastq = None 196 self.illumina_fastq = None
193 else: 197 self.illumina_length_mean = None
198 self.illumina_read_count = None
199 else:
200 self.illumina_fastq = self.analysis_name
201 self.illumina_bases = 0
202 self.illumina_length_mean = 0
203 self.illumina_read_count = 0
204 self.ont_bases = None
194 self.ont_raw_fastq = None 205 self.ont_raw_fastq = None
195 self.illumina_fastq = self.analysis_name
196 self.ont_read_count = None
197 206
198 # Actions 207 # Actions
199 self.did_guppy_ont_fast5 = False 208 self.did_guppy_ont_fast5 = False
200 self.did_qcat_ont_fastq = False 209 self.did_qcat_ont_fastq = False
201 self.ofh.write("self.read_type: %s\n" % str(self.read_type)) 210 self.ofh.write("self.read_type: %s\n" % str(self.read_type))
202 if self.read_type == 'ONT': 211 if self.read_type == 'ONT':
203 self.info_ont_fastq(self.fastq_file) 212 self.info_ont_fastq(self.ont_file)
204 else: 213 else:
205 self.info_illumina_fastq(self.fastq_file) 214 self.info_illumina_fastq([self.illumina_forward_read_file, self.illumina_reverse_read_file])
206 self.load_contig_info() 215 self.load_contig_info()
207 216
208 def run_command(self, command): 217 def run_command(self, command):
209 self.ofh.write("\nXXXXXX In run_command, command:\n%s\n\n" % str(command)) 218 self.ofh.write("\nXXXXXX In run_command, command:\n%s\n\n" % str(command))
210 try: 219 try:
228 237
229 def load_contig_info(self): 238 def load_contig_info(self):
230 self.contig_info = pandas.Series(dtype=object) 239 self.contig_info = pandas.Series(dtype=object)
231 self.contig_info[self.read_type] = pandas.read_csv(self.contig_coverage_file, header=None, index_col=None, sep='\t').sort_values(1, axis=0, ascending=False) 240 self.contig_info[self.read_type] = pandas.read_csv(self.contig_coverage_file, header=None, index_col=None, sep='\t').sort_values(1, axis=0, ascending=False)
232 self.contig_info[self.read_type].columns = ['contig', 'size', 'coverage'] 241 self.contig_info[self.read_type].columns = ['contig', 'size', 'coverage']
233 self.mean_coverage = (self.contig_info[self.read_type].iloc[:, 1] * self.contig_info[self.read_type].iloc[:, 2]).sum() / self.contig_info[self.read_type].iloc[:, 1].sum() 242 mean_coverage = (self.contig_info[self.read_type].iloc[:, 1] * self.contig_info[self.read_type].iloc[:, 2]).sum() / self.contig_info[self.read_type].iloc[:, 1].sum()
234 if self.mean_coverage <= self.ont_coverage_min: 243 if mean_coverage <= self.ont_coverage_min:
235 warning = '%s mean coverage ({:.0f}X) is less than the recommended minimum ({:.0f}X).'.format(self.mean_coverage, self.ont_coverage_min) % self.read_type 244 warning = '%s mean coverage ({:.0f}X) is less than the recommended minimum ({:.0f}X).'.format(mean_coverage, self.ont_coverage_min) % self.read_type
236 self.assembly_notes = self.assembly_notes.append(pandas.Series(warning)) 245 self.assembly_notes = self.assembly_notes.append(pandas.Series(warning))
237 # Report if some contigs have low coverage. 246 # Report if some contigs have low coverage.
238 low_coverage = self.contig_info[self.read_type].loc[self.contig_info[self.read_type]['coverage'] < self.ont_coverage_min, :] 247 low_coverage = self.contig_info[self.read_type].loc[self.contig_info[self.read_type]['coverage'] < self.ont_coverage_min, :]
239 if low_coverage.shape[0] >= 0: 248 if low_coverage.shape[0] >= 0:
240 for contig_i in range(low_coverage.shape[0]): 249 for contig_i in range(low_coverage.shape[0]):
241 warning = '%s coverage of {:s} ({:.0f}X) is less than the recommended minimum ({:.0f}X).'.format(low_coverage.iloc[contig_i, 0], low_coverage.iloc[contig_i, 2], self.ont_coverage_min) % self.read_type 250 warning = '%s coverage of {:s} ({:.0f}X) is less than the recommended minimum ({:.0f}X).'.format(low_coverage.iloc[contig_i, 0], low_coverage.iloc[contig_i, 2], self.ont_coverage_min) % self.read_type
242 self.assembly_notes = self.assembly_notes.append(pandas.Series(warning)) 251 self.assembly_notes = self.assembly_notes.append(pandas.Series(warning))
243 # See if some contigs have anolously low coverage. 252 # See if some contigs have anonymously low coverage.
244 fold_coverage = self.contig_info[self.read_type]['coverage'] / self.mean_coverage 253 fold_coverage = self.contig_info[self.read_type]['coverage'] / mean_coverage
245 low_coverage = self.contig_info[self.read_type].loc[fold_coverage < 1 / 5, :] 254 low_coverage = self.contig_info[self.read_type].loc[fold_coverage < 1 / 5, :]
246 if low_coverage.shape[0] >= 0: 255 if low_coverage.shape[0] >= 0:
247 for contig_i in range(low_coverage.shape[0]): 256 for contig_i in range(low_coverage.shape[0]):
248 warning = '%s coverage of {:s} ({:.0f}X) is less than 1/5 the mean coverage ({:.0f}X).'.format(low_coverage.iloc[contig_i, 0], low_coverage.iloc[contig_i, 2], self.mean_coverage) % self.read_type 257 warning = '%s coverage of {:s} ({:.0f}X) is less than 1/5 the mean coverage ({:.0f}X).'.format(low_coverage.iloc[contig_i, 0], low_coverage.iloc[contig_i, 2], mean_coverage) % self.read_type
249 self.assembly_notes = self.assembly_notes.append(pandas.Series(warning)) 258 self.assembly_notes = self.assembly_notes.append(pandas.Series(warning))
250 259
251 def load_fasta(self, fasta): 260 def load_fasta(self, fasta):
252 sequence = pandas.Series(dtype=object) 261 sequence = pandas.Series(dtype=object)
253 for contig in SeqIO.parse(fasta, 'fasta'): 262 for contig in SeqIO.parse(fasta, 'fasta'):
255 return sequence 264 return sequence
256 265
257 def load_assembly(self): 266 def load_assembly(self):
258 self.assembly = self.load_fasta(self.assembly_fasta_file) 267 self.assembly = self.load_fasta(self.assembly_fasta_file)
259 self.num_assembly_contigs = len(self.assembly) 268 self.num_assembly_contigs = len(self.assembly)
260 for i in self.assembly: 269 self.assembly_size = self.format_kmg(sum([len(x) for x in self.assembly]), decimals=1)
261 self.assembly_size += len(i.seq) 270
262 self.assembly_size = self.format_kmg(self.assembly_size, decimals=1) 271 def info_illumina_fastq(self, illumina_read_files):
263
264 def info_illumina_fastq(self, fastq_file):
265 self.ofh.write("\nXXXXXX In info_illumina_fastq\n\n") 272 self.ofh.write("\nXXXXXX In info_illumina_fastq\n\n")
266 if self.illumina_length_mean is None:
267 return
268 if self.gzipped: 273 if self.gzipped:
269 opener = 'gunzip -c' 274 opener = 'gunzip -c'
270 else: 275 else:
271 opener = 'cat' 276 opener = 'cat'
272 command = ' '.join([opener, 277 for fastq_file in illumina_read_files:
273 fastq_file, 278 command = ' '.join([opener,
274 '| awk \'{getline;s += length($1);getline;getline;}END{print s/(NR/4)"\t"(NR/4)"\t"s}\'']) 279 fastq_file,
275 output = self.run_command(command) 280 '| awk \'{getline;s += length($1);getline;getline;}END{print s/(NR/4)"\t"(NR/4)"\t"s}\''])
276 self.ofh.write("output:\n%s\n" % str(output)) 281 output = self.run_command(command)
277 self.ofh.write("re.split('\\t', self.run_command(command)[0]:\n%s\n" % str(re.split('\\t', self.run_command(command)[0]))) 282 self.ofh.write("output:\n%s\n" % str(output))
278 values = [] 283 self.ofh.write("re.split('\\t', self.run_command(command)[0]:\n%s\n" % str(re.split('\\t', self.run_command(command)[0])))
279 for i in re.split('\\t', self.run_command(command)[0]): 284 values = []
280 if i == '': 285 for i in re.split('\\t', self.run_command(command)[0]):
281 values.append(float('nan')) 286 if i == '':
282 else: 287 values.append(float('nan'))
283 values.append(float(i)) 288 else:
284 self.ofh.write("values:\n%s\n" % str(values)) 289 values.append(float(i))
285 self.ofh.write("values[0]:\n%s\n" % str(values[0])) 290 self.ofh.write("values:\n%s\n" % str(values))
286 self.illumina_length_mean += values[0] 291 self.ofh.write("values[0]:\n%s\n" % str(values[0]))
287 self.ofh.write("values[1]:\n%s\n" % str(values[1])) 292 self.illumina_length_mean += values[0]
288 self.illumina_read_count += int(values[1]) 293 self.ofh.write("values[1]:\n%s\n" % str(values[1]))
289 self.ofh.write("values[2]:\n%s\n" % str(values[2])) 294 self.illumina_read_count += int(values[1])
290 self.illumina_bases += int(values[2]) 295 self.ofh.write("values[2]:\n%s\n" % str(values[2]))
291 self.illumina_length_mean /= 1 296 self.illumina_bases += int(values[2])
297 self.illumina_length_mean /= 2
292 self.illumina_bases = self.format_kmg(self.illumina_bases, decimals=1) 298 self.illumina_bases = self.format_kmg(self.illumina_bases, decimals=1)
293 299
294 def start_doc(self): 300 def start_doc(self):
295 header_text = 'Analysis of ' + self.analysis_name 301 header_text = 'Analysis of ' + self.analysis_name
296 self.doc = MdUtils(file_name=self.report_md, title=header_text) 302 self.doc = MdUtils(file_name=self.report_md, title=header_text)
452 else: 458 else:
453 return string 459 return string
454 460
455 def add_contig_info(self): 461 def add_contig_info(self):
456 self.ofh.write("\nXXXXXX In add_contig_info\n\n") 462 self.ofh.write("\nXXXXXX In add_contig_info\n\n")
457 if self.contig_info is None: 463 if self.contig_info is None or self.read_type not in self.contig_info.index:
458 return 464 return
459 for method in ['ONT', 'Illumina']: 465 self.doc.new_line()
460 if method not in self.contig_info.index: 466 self.doc.new_header(2, 'Assembly coverage by ' + self.read_type)
461 continue 467 Table_List = ["Contig", "Length (bp)", "Coverage (X)"]
462 self.doc.new_line() 468 formatted = self.contig_info[self.read_type].copy()
463 self.doc.new_header(2, 'Assembly coverage by ' + method) 469 formatted.iloc[:, 1] = formatted.iloc[:, 1].apply(lambda x: '{:,}'.format(x))
464 Table_List = ["Contig", "Length (bp)", "Coverage (X)"] 470 for i in range(self.contig_info[self.read_type].shape[0]):
465 formatted = self.contig_info[method].copy() 471 Table_List = Table_List + formatted.iloc[i, :].values.tolist()
466 formatted.iloc[:, 1] = formatted.iloc[:, 1].apply(lambda x: '{:,}'.format(x)) 472 row_count = int(len(Table_List) / 3)
467 for i in range(self.contig_info[method].shape[0]): 473 self.doc.new_table(columns=3, rows=row_count, text=Table_List, text_align='left')
468 Table_List = Table_List + formatted.iloc[i, :].values.tolist()
469 row_count = int(len(Table_List) / 3)
470 self.doc.new_table(columns=3, rows=row_count, text=Table_List, text_align='left')
471 474
472 def add_assembly_notes(self): 475 def add_assembly_notes(self):
473 self.ofh.write("\nXXXXXX In add_assembly_notes\n\n") 476 self.ofh.write("\nXXXXXX In add_assembly_notes\n\n")
474 if len(self.assembly_notes) == 0: 477 if len(self.assembly_notes) == 0:
475 return 478 return
792 if self.did_guppy_ont_fast5: 795 if self.did_guppy_ont_fast5:
793 methods += ['ONT reads were basecalled using guppy'] 796 methods += ['ONT reads were basecalled using guppy']
794 if self.did_qcat_ont_fastq: 797 if self.did_qcat_ont_fastq:
795 methods += ['ONT reads were demultiplexed and trimmed using qcat'] 798 methods += ['ONT reads were demultiplexed and trimmed using qcat']
796 self.methods[self.basecalling_methods_title] = pandas.Series(methods) 799 self.methods[self.basecalling_methods_title] = pandas.Series(methods)
797 # self.add_illumina_library_information() 800 self.add_illumina_library_information()
801 self.add_assembly_information()
798 self.add_contig_info() 802 self.add_contig_info()
799 self.evaluate_assembly() 803 self.evaluate_assembly()
800 self.add_assembly_information()
801 if self.assembler_version is not None: 804 if self.assembler_version is not None:
802 if self.read_type == 'ONT': 805 if self.read_type == 'ONT':
803 method = 'ONT reads were assembled using %s' % self.assembler_version 806 method = 'ONT reads were assembled using %s' % self.assembler_version
804 self.methods[self.assembly_methods_title] = self.methods[self.assembly_methods_title].append(pandas.Series(method)) 807 self.methods[self.assembly_methods_title] = self.methods[self.assembly_methods_title].append(pandas.Series(method))
805 # Pull in the assembly summary and look at the coverage. 808 # Pull in the assembly summary and look at the coverage.
810 open_contig_ids = open_contigs.index.values 813 open_contig_ids = open_contigs.index.values
811 warning = 'Flye reported {:d} open contigs ({:s}); assembly may be incomplete.'.format(open_contigs.shape[0], ', '.join(open_contig_ids)) 814 warning = 'Flye reported {:d} open contigs ({:s}); assembly may be incomplete.'.format(open_contigs.shape[0], ', '.join(open_contig_ids))
812 self.assembly_notes = self.assembly_notes.append(pandas.Series(warning)) 815 self.assembly_notes = self.assembly_notes.append(pandas.Series(warning))
813 else: 816 else:
814 method = 'Illumina reads were assembled using %s' % self.assembler_version 817 method = 'Illumina reads were assembled using %s' % self.assembler_version
815 if self.did_medaka_ont_assembly: 818 method = 'The genome assembly was polished using ONT reads and medaka.'
816 method = 'the genome assembly was polished using ont reads and medaka.' 819 self.methods[self.assembly_methods_title] = self.methods[self.assembly_methods_title].append(pandas.series(method))
817 self.methods[self.assembly_methods_title] = self.methods[self.assembly_methods_title].append(pandas.series(method))
818 self.add_assembly_notes() 820 self.add_assembly_notes()
819 821
820 def make_tex(self): 822 def make_tex(self):
821 self.doc.new_table_of_contents(table_title='detailed run information', depth=2, marker="tableofcontents") 823 self.doc.new_table_of_contents(table_title='detailed run information', depth=2, marker="tableofcontents")
822 text = self.doc.file_data_text 824 text = self.doc.file_data_text
867 parser.add_argument('--contig_coverage_file', action='store', dest='contig_coverage_file', help='Contig coverage TSV file') 869 parser.add_argument('--contig_coverage_file', action='store', dest='contig_coverage_file', help='Contig coverage TSV file')
868 parser.add_argument('--dbkey', action='store', dest='dbkey', help='Reference genome identifier') 870 parser.add_argument('--dbkey', action='store', dest='dbkey', help='Reference genome identifier')
869 parser.add_argument('--dnadiff_snps_file', action='store', dest='dnadiff_snps_file', help='DNAdiff snps tabular file') 871 parser.add_argument('--dnadiff_snps_file', action='store', dest='dnadiff_snps_file', help='DNAdiff snps tabular file')
870 parser.add_argument('--dnadiff_version', action='store', dest='dnadiff_version', default=None, help='DNAdiff version string') 872 parser.add_argument('--dnadiff_version', action='store', dest='dnadiff_version', default=None, help='DNAdiff version string')
871 parser.add_argument('--errors_file', action='store', dest='errors_file', default=None, help='AMR mutations errors encountered txt file') 873 parser.add_argument('--errors_file', action='store', dest='errors_file', default=None, help='AMR mutations errors encountered txt file')
872 parser.add_argument('--fastq_file', action='store', dest='fastq_file', help='Input sample')
873 parser.add_argument('--feature_bed_dir', action='store', dest='feature_bed_dir', help='Directory of best feature hits bed files') 874 parser.add_argument('--feature_bed_dir', action='store', dest='feature_bed_dir', help='Directory of best feature hits bed files')
874 parser.add_argument('--feature_png_dir', action='store', dest='feature_png_dir', help='Directory of best feature hits png files') 875 parser.add_argument('--feature_png_dir', action='store', dest='feature_png_dir', help='Directory of best feature hits png files')
875 parser.add_argument('--flye_assembly_info_file', action='store', dest='flye_assembly_info_file', default=None, help='Flye assembly info tabular file') 876 parser.add_argument('--flye_assembly_info_file', action='store', dest='flye_assembly_info_file', default=None, help='Flye assembly info tabular file')
876 parser.add_argument('--genome_insertions_file', action='store', dest='genome_insertions_file', help='Genome insertions BED file') 877 parser.add_argument('--genome_insertions_file', action='store', dest='genome_insertions_file', help='Genome insertions BED file')
877 parser.add_argument('--gzipped', action='store_true', dest='gzipped', default=False, help='Input sample is gzipped') 878 parser.add_argument('--gzipped', action='store_true', dest='gzipped', default=False, help='Sample(s) is/are gzipped')
879 parser.add_argument('--illumina_forward_read_file', action='store', dest='illumina_forward_read_file', help='Illumina forward read file')
880 parser.add_argument('--illumina_reverse_read_file', action='store', dest='illumina_reverse_read_file', help='Illumina reverse read file')
878 parser.add_argument('--kraken2_report_file', action='store', dest='kraken2_report_file', default=None, help='kraken2 report file') 881 parser.add_argument('--kraken2_report_file', action='store', dest='kraken2_report_file', default=None, help='kraken2 report file')
879 parser.add_argument('--kraken2_version', action='store', dest='kraken2_version', default=None, help='kraken2 version string') 882 parser.add_argument('--kraken2_version', action='store', dest='kraken2_version', default=None, help='kraken2 version string')
880 parser.add_argument('--minimap2_version', action='store', dest='minimap2_version', default=None, help='minimap2 version string') 883 parser.add_argument('--minimap2_version', action='store', dest='minimap2_version', default=None, help='minimap2 version string')
881 parser.add_argument('--mutation_regions_bed_file', action='store', dest='mutation_regions_bed_file', help='AMR mutation regions BRD file') 884 parser.add_argument('--mutation_regions_bed_file', action='store', dest='mutation_regions_bed_file', help='AMR mutation regions BRD file')
882 parser.add_argument('--mutation_regions_dir', action='store', dest='mutation_regions_dir', help='Directory of mutation regions TSV files') 885 parser.add_argument('--mutation_regions_dir', action='store', dest='mutation_regions_dir', help='Directory of mutation regions TSV files')
886 parser.add_argument('--ont_file', action='store', dest='ont_file', help='ONT single read file')
883 parser.add_argument('--pima_css', action='store', dest='pima_css', help='PIMA css stypesheet') 887 parser.add_argument('--pima_css', action='store', dest='pima_css', help='PIMA css stypesheet')
884 parser.add_argument('--plasmids_file', action='store', dest='plasmids_file', default=None, help='pChunks plasmids TSV file') 888 parser.add_argument('--plasmids_file', action='store', dest='plasmids_file', default=None, help='pChunks plasmids TSV file')
885 parser.add_argument('--quast_report_file', action='store', dest='quast_report_file', help='Quast report tabular file') 889 parser.add_argument('--quast_report_file', action='store', dest='quast_report_file', help='Quast report tabular file')
886 parser.add_argument('--read_type', action='store', dest='read_type', help='Sample read type (ONT or Illumina)') 890 parser.add_argument('--read_type', action='store', dest='read_type', help='Sample read type (ONT or Illumina)')
887 parser.add_argument('--reference_insertions_file', action='store', dest='reference_insertions_file', help='Reference insertions BED file') 891 parser.add_argument('--reference_insertions_file', action='store', dest='reference_insertions_file', help='Reference insertions BED file')
929 args.contig_coverage_file, 933 args.contig_coverage_file,
930 args.dbkey, 934 args.dbkey,
931 args.dnadiff_snps_file, 935 args.dnadiff_snps_file,
932 args.dnadiff_version, 936 args.dnadiff_version,
933 args.errors_file, 937 args.errors_file,
934 args.fastq_file,
935 feature_bed_files, 938 feature_bed_files,
936 feature_png_files, 939 feature_png_files,
937 args.flye_assembly_info_file, 940 args.flye_assembly_info_file,
938 args.genome_insertions_file, 941 args.genome_insertions_file,
939 args.gzipped, 942 args.gzipped,
943 args.illumina_forward_read_file,
944 args.illumina_reverse_read_file,
940 args.kraken2_report_file, 945 args.kraken2_report_file,
941 args.kraken2_version, 946 args.kraken2_version,
942 args.minimap2_version, 947 args.minimap2_version,
943 args.mutation_regions_bed_file, 948 args.mutation_regions_bed_file,
944 mutation_regions_files, 949 mutation_regions_files,
950 args.ont_file,
945 args.pima_css, 951 args.pima_css,
946 args.plasmids_file, 952 args.plasmids_file,
947 args.quast_report_file, 953 args.quast_report_file,
948 args.read_type, 954 args.read_type,
949 args.reference_insertions_file, 955 args.reference_insertions_file,