Mercurial > repos > greg > pima_report

comparison pima_report.py @ 22:13a9c8ecd30e draft

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Uploaded
author greg
date Thu, 13 Apr 2023 18:33:19 +0000
parents 667b253329c6
children d89b7d47a85a
comparison
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21:667b253329c6 22:13a9c8ecd30e
540 for circos_file in self.circos_files: 540 for circos_file in self.circos_files:
541 contig = os.path.basename(circos_file) 541 contig = os.path.basename(circos_file)
542 contig_title = 'Alignment to %s' % contig 542 contig_title = 'Alignment to %s' % contig
543 self.doc.new_line() 543 self.doc.new_line()
544 self.doc.new_header(level=3, title=contig_title) 544 self.doc.new_header(level=3, title=contig_title)
545 self.doc.new_line('Blue indicates aligned sequences (to the reference) and yellow indicates missing sequences')
545 self.doc.new_line(self.doc.new_inline_image(text='contig_title', path=os.path.abspath(circos_file))) 546 self.doc.new_line(self.doc.new_inline_image(text='contig_title', path=os.path.abspath(circos_file)))
546 self.doc.new_line('<div style="page-break-after: always;"></div>') 547 self.doc.new_line('<div style="page-break-after: always;"></div>')
547 self.doc.new_line() 548 self.doc.new_line()
548 if self.dbkey == 'ref_genome': 549 if self.dbkey == 'ref_genome':
549 headers = ["* Chromosome - NC_007530.2 Bacillus anthracis str. 'Ames Ancestor', complete sequence", 550 headers = ["* Chromosome - NC_007530.2 Bacillus anthracis str. 'Ames Ancestor', complete sequence",