Mercurial > repos > greg > pima_report

comparison pima_report.py @ 32:163260afc1b1 draft

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author greg
date Thu, 31 Aug 2023 18:30:13 +0000
parents a859de7cce94
children f5a9f1969199
comparison
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31:a859de7cce94 32:163260afc1b1
462 462
463 def add_alignment(self): 463 def add_alignment(self):
464 if self.quast_report_file is not None: 464 if self.quast_report_file is not None:
465 # Process quast values. 465 # Process quast values.
466 quast_report = pandas.read_csv(self.quast_report_file, header=0, index_col=0, sep='\t') 466 quast_report = pandas.read_csv(self.quast_report_file, header=0, index_col=0, sep='\t')
467 quast_mismatches = int(float(quast_report.loc['# mismatches per 100 kbp', :][0]) * (float(quast_report.loc['Total length (>= 0 bp)', :][0]) / 100000.)) 467 try:
468 quast_indels = int(float(quast_report.loc['# indels per 100 kbp', :][0]) * (float(quast_report.loc['Total length (>= 0 bp)', :][0]) / 100000.)) 468 quast_mismatches = int(float(quast_report.loc['# mismatches per 100 kbp', :][0]) * (float(quast_report.loc['Total length (>= 0 bp)', :][0]) / 100000.))
469 self.doc.new_line() 469 quast_indels = int(float(quast_report.loc['# indels per 100 kbp', :][0]) * (float(quast_report.loc['Total length (>= 0 bp)', :][0]) / 100000.))
470 self.doc.new_header(level=2, title=self.alignment_title) 470 self.doc.new_line()
471 self.doc.new_line() 471 self.doc.new_header(level=2, title=self.alignment_title)
472 self.doc.new_header(level=3, title=self.snp_indel_title) 472 self.doc.new_line()
473 Table_1 = [ 473 self.doc.new_header(level=3, title=self.snp_indel_title)
474 "Category", 474 Table_1 = [
475 "Quantity", 475 "Category",
476 'SNPs', 476 "Quantity",
477 '{:,}'.format(quast_mismatches), 477 'SNPs',
478 'Small indels', 478 '{:,}'.format(quast_mismatches),
479 '{:,}'.format(quast_indels) 479 'Small indels',
480 ] 480 '{:,}'.format(quast_indels)
481 ]
482 except Exception:
483 # Likely a high dissimilarity bewteen the sample
484 # and the reference, resulting in a failed alignment.
485 pass
481 self.doc.new_table(columns=2, rows=3, text=Table_1, text_align='left') 486 self.doc.new_table(columns=2, rows=3, text=Table_1, text_align='left')
482 self.doc.new_line('<div style="page-break-after: always;"></div>') 487 self.doc.new_line('<div style="page-break-after: always;"></div>')
483 self.doc.new_line() 488 self.doc.new_line()
484 # TODO: self.alignment_notes is not currently populated. 489 # TODO: self.alignment_notes is not currently populated.
485 if len(self.alignment_notes) > 0: 490 if len(self.alignment_notes) > 0: