Mercurial > repos > greg > pima_report

comparison pima_report.py @ 25:4986a7fb2145 draft

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Uploaded
author greg
date Thu, 20 Apr 2023 18:47:01 +0000
parents 803e5965ed20
children 46edd7435555
comparison
equal deleted inserted replaced
24:803e5965ed20 25:4986a7fb2145
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('Blue color indicates query sequences aligned to the reference sequence, which is shown in yellow')
546 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)))
547 self.doc.new_line('<div style="page-break-after: always;"></div>') 547 self.doc.new_line('<div style="page-break-after: always;"></div>')
548 self.doc.new_line() 548 self.doc.new_line()
549 if self.dbkey == 'ref_genome': 549 if self.dbkey == 'ref_genome':
550 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",
712 if amr_deletions.shape[0] > 0: 712 if amr_deletions.shape[0] > 0:
713 amr_deletions.columns = ['contig', 'start', 'stop', 'name', 'type', 'drug', 'note'] 713 amr_deletions.columns = ['contig', 'start', 'stop', 'name', 'type', 'drug', 'note']
714 amr_deletions = amr_deletions.loc[amr_deletions['type'].isin(['large-deletion', 'any']), :] 714 amr_deletions = amr_deletions.loc[amr_deletions['type'].isin(['large-deletion', 'any']), :]
715 self.doc.new_line() 715 self.doc.new_line()
716 self.doc.new_header(level=2, title=self.large_indel_title) 716 self.doc.new_header(level=2, title=self.large_indel_title)
717 self.doc.new_line('This section is informative only when your idolates were identified as *Bacillus anthracis* strains') 717 self.doc.new_line('This section is informative only when your isolates were identified as *Bacillus anthracis* strains')
718 for genome in ['Reference insertions', 'Query insertions']: 718 for genome in ['Reference insertions', 'Query insertions']:
719 genome_indels = large_indels[genome].copy() 719 genome_indels = large_indels[genome].copy()
720 self.doc.new_line() 720 self.doc.new_line()
721 self.doc.new_header(level=3, title=genome) 721 self.doc.new_header(level=3, title=genome)
722 if (genome_indels.shape[0] == 0): 722 if (genome_indels.shape[0] == 0):