Mercurial > repos > greg > pima_report

comparison pima_report.py @ 20:4fe8c35cd176 draft

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author greg
date Thu, 30 Mar 2023 20:41:18 +0000
parents c509e6819795
children 667b253329c6
comparison
equal deleted inserted replaced
19:c509e6819795 20:4fe8c35cd176
526 if len(self.circos_files) > 0: 526 if len(self.circos_files) > 0:
527 # Add circos PNG files. 527 # Add circos PNG files.
528 for circos_file in self.circos_files: 528 for circos_file in self.circos_files:
529 contig = os.path.basename(circos_file) 529 contig = os.path.basename(circos_file)
530 contig_title = 'Alignment to %s' % contig 530 contig_title = 'Alignment to %s' % contig
531 self.doc.new_line('Blue indicates aligned sequences (to the reference) and yellow indicates missing sequences')
532 self.doc.new_line() 531 self.doc.new_line()
533 self.doc.new_header(level=3, title=contig_title) 532 self.doc.new_header(level=3, title=contig_title)
533 self.doc.new_line('Blue indicates aligned sequences (to the reference) and yellow indicates missing sequences')
534 self.doc.new_line(self.doc.new_inline_image(text='contig_title', path=os.path.abspath(circos_file))) 534 self.doc.new_line(self.doc.new_inline_image(text='contig_title', path=os.path.abspath(circos_file)))
535 self.doc.new_line('<div style="page-break-after: always;"></div>') 535 self.doc.new_line('<div style="page-break-after: always;"></div>')
536 self.doc.new_line() 536 self.doc.new_line()
537 method = 'The genome assembly was aligned against the reference sequencing using dnadiff version %s.' % self.dnadiff_version 537 method = 'The genome assembly was aligned against the reference sequencing using dnadiff version %s.' % self.dnadiff_version
538 self.methods[self.reference_methods_title] = self.methods[self.reference_methods_title].append(pandas.Series(method)) 538 self.methods[self.reference_methods_title] = self.methods[self.reference_methods_title].append(pandas.Series(method))