Mercurial > repos > greg > pima_report

comparison pima_report.py @ 11:4a7c31f28197 draft

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Uploaded
author greg
date Thu, 09 Mar 2023 18:34:01 +0000
parents 7c4077c9b3ad
children 99613333fd1f
comparison
equal deleted inserted replaced
10:7c4077c9b3ad 11:4a7c31f28197
436 Table_List = Table_List + row.tolist() 436 Table_List = Table_List + row.tolist()
437 row_count = int(len(Table_List) / 4) 437 row_count = int(len(Table_List) / 4)
438 self.doc.new_table(columns=4, rows=row_count, text=Table_List, text_align='left') 438 self.doc.new_table(columns=4, rows=row_count, text=Table_List, text_align='left')
439 if self.contamination_methods_title not in self.methods: 439 if self.contamination_methods_title not in self.methods:
440 self.methods[self.contamination_methods_title] = '' 440 self.methods[self.contamination_methods_title] = ''
441 method = 'Kraken2 version %s was used to assign the raw reads into taxa.' % self.kraken2_version 441 method = '%s was used to assign the raw reads into taxa.' % self.kraken2_version.rstrip('report')
442 self.methods[self.contamination_methods_title] = self.methods[self.contamination_methods_title].append(pandas.Series(method)) 442 self.methods[self.contamination_methods_title] = self.methods[self.contamination_methods_title].append(pandas.Series(method))
443 443
444 def add_alignment(self): 444 def add_alignment(self):
445 self.ofh.write("\nXXXXXX In add_alignment\n\n") 445 self.ofh.write("\nXXXXXX In add_alignment\n\n")
446 # TODO: implement the draw_circos function for this. 446 # TODO: implement the draw_circos function for this.
521 self.ofh.write("row_count: %s\n" % str(row_count)) 521 self.ofh.write("row_count: %s\n" % str(row_count))
522 self.doc.new_line() 522 self.doc.new_line()
523 self.ofh.write("Before new_table, len(Table_List):: %s\n" % str(len(Table_List))) 523 self.ofh.write("Before new_table, len(Table_List):: %s\n" % str(len(Table_List)))
524 self.doc.new_table(columns=5, rows=row_count, text=Table_List, text_align='left') 524 self.doc.new_table(columns=5, rows=row_count, text=Table_List, text_align='left')
525 if self.blastn_version is not None: 525 if self.blastn_version is not None:
526 blastn_version = 'The genome assembly was queried for features using blastn version %s.' % self.blastn_version 526 blastn_version = 'The genome assembly was queried for features using %s.' % self.blastn_version
527 bedtools_version = 'Feature hits were clustered using bedtools and the highest scoring hit for each cluster was reported.' 527 bedtools_version = 'Feature hits were clustered using bedtools and the highest scoring hit for each cluster was reported.'
528 method = '%s %s' % (blastn_version, bedtools_version) 528 method = '%s %s' % (blastn_version, bedtools_version)
529 self.methods[self.feature_methods_title] = self.methods[self.feature_methods_title].append(pandas.Series(method)) 529 self.methods[self.feature_methods_title] = self.methods[self.feature_methods_title].append(pandas.Series(method))
530 530
531 def add_feature_plots(self): 531 def add_feature_plots(self):
742 self.add_illumina_library_information() 742 self.add_illumina_library_information()
743 self.add_contig_info() 743 self.add_contig_info()
744 self.evaluate_assembly() 744 self.evaluate_assembly()
745 self.add_assembly_information() 745 self.add_assembly_information()
746 if self.flye_assembly_info_file is not None: 746 if self.flye_assembly_info_file is not None:
747 method = 'ONT reads were assembled using %s' % self.flye_version 747 method = 'ONT reads were assembled using %s' % self.flye_version.rstrip('assembly info')
748 self.methods[self.assembly_methods_title] = self.methods[self.assembly_methods_title].append(pandas.Series(method)) 748 self.methods[self.assembly_methods_title] = self.methods[self.assembly_methods_title].append(pandas.Series(method))
749 # Pull in the assembly summary and look at the coverage. 749 # Pull in the assembly summary and look at the coverage.
750 assembly_info = pandas.read_csv(self.flye_assembly_info_file, header=0, index_col=0, sep='\t') 750 assembly_info = pandas.read_csv(self.flye_assembly_info_file, header=0, index_col=0, sep='\t')
751 # Look for non-circular contigs. 751 # Look for non-circular contigs.
752 open_contigs = assembly_info.loc[assembly_info['circ.'] == 'N', :] 752 open_contigs = assembly_info.loc[assembly_info['circ.'] == 'N', :]