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comparison pima_report.py @ 27:ddc056cf16bf draft

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author greg
date Tue, 25 Apr 2023 21:30:56 +0000
parents 46edd7435555
children 27485e70ed2b
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26:46edd7435555 27:ddc056cf16bf
814 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))
815 self.assembly_notes = self.assembly_notes.append(pandas.Series(warning)) 815 self.assembly_notes = self.assembly_notes.append(pandas.Series(warning))
816 else: 816 else:
817 method = 'Illumina reads were assembled using %s' % self.assembler_version 817 method = 'Illumina reads were assembled using %s' % self.assembler_version
818 method = 'The genome assembly was polished using ONT reads and medaka.' 818 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)) 819 self.methods[self.assembly_methods_title] = self.methods[self.assembly_methods_title].append(pandas.Series(method))
820 self.add_assembly_notes() 820 self.add_assembly_notes()
821 821
822 def make_tex(self): 822 def make_tex(self):
823 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")
824 text = self.doc.file_data_text 824 text = self.doc.file_data_text