comparison pima_report.py @ 11:4a7c31f28197 draft

Uploaded

10:7c4077c9b3ad

            Table_List = Table_List + row.tolist()
        row_count = int(len(Table_List) / 4)
        self.doc.new_table(columns=4, rows=row_count, text=Table_List, text_align='left')
        if self.contamination_methods_title not in self.methods:
            self.methods[self.contamination_methods_title] = ''
        method = 'Kraken2 version %s was used to assign the raw reads into taxa.' % self.kraken2_version
        self.methods[self.contamination_methods_title] = self.methods[self.contamination_methods_title].append(pandas.Series(method))

    def add_alignment(self):
        self.ofh.write("\nXXXXXX In add_alignment\n\n")
        # TODO: implement the draw_circos function for this.

                self.ofh.write("row_count: %s\n" % str(row_count))
                self.doc.new_line()
                self.ofh.write("Before new_table, len(Table_List):: %s\n" % str(len(Table_List)))
                self.doc.new_table(columns=5, rows=row_count, text=Table_List, text_align='left')
        if self.blastn_version is not None:
            blastn_version = 'The genome assembly was queried for features using blastn version %s.' % self.blastn_version
        bedtools_version = 'Feature hits were clustered using bedtools and the highest scoring hit for each cluster was reported.'
        method = '%s  %s' % (blastn_version, bedtools_version)
        self.methods[self.feature_methods_title] = self.methods[self.feature_methods_title].append(pandas.Series(method))

    def add_feature_plots(self):

        self.add_illumina_library_information()
        self.add_contig_info()
        self.evaluate_assembly()
        self.add_assembly_information()
        if self.flye_assembly_info_file is not None:
            method = 'ONT reads were assembled using %s' % self.flye_version
            self.methods[self.assembly_methods_title] = self.methods[self.assembly_methods_title].append(pandas.Series(method))
            # Pull in the assembly summary and look at the coverage.
            assembly_info = pandas.read_csv(self.flye_assembly_info_file, header=0, index_col=0, sep='\t')
            # Look for non-circular contigs.
            open_contigs = assembly_info.loc[assembly_info['circ.'] == 'N', :]

11:4a7c31f28197

            Table_List = Table_List + row.tolist()
        row_count = int(len(Table_List) / 4)
        self.doc.new_table(columns=4, rows=row_count, text=Table_List, text_align='left')
        if self.contamination_methods_title not in self.methods:
            self.methods[self.contamination_methods_title] = ''
        method = '%s was used to assign the raw reads into taxa.' % self.kraken2_version.rstrip('report')
        self.methods[self.contamination_methods_title] = self.methods[self.contamination_methods_title].append(pandas.Series(method))

    def add_alignment(self):
        self.ofh.write("\nXXXXXX In add_alignment\n\n")
        # TODO: implement the draw_circos function for this.

                self.ofh.write("row_count: %s\n" % str(row_count))
                self.doc.new_line()
                self.ofh.write("Before new_table, len(Table_List):: %s\n" % str(len(Table_List)))
                self.doc.new_table(columns=5, rows=row_count, text=Table_List, text_align='left')
        if self.blastn_version is not None:
            blastn_version = 'The genome assembly was queried for features using %s.' % self.blastn_version
        bedtools_version = 'Feature hits were clustered using bedtools and the highest scoring hit for each cluster was reported.'
        method = '%s  %s' % (blastn_version, bedtools_version)
        self.methods[self.feature_methods_title] = self.methods[self.feature_methods_title].append(pandas.Series(method))

    def add_feature_plots(self):

        self.add_illumina_library_information()
        self.add_contig_info()
        self.evaluate_assembly()
        self.add_assembly_information()
        if self.flye_assembly_info_file is not None:
            method = 'ONT reads were assembled using %s' % self.flye_version.rstrip('assembly info')
            self.methods[self.assembly_methods_title] = self.methods[self.assembly_methods_title].append(pandas.Series(method))
            # Pull in the assembly summary and look at the coverage.
            assembly_info = pandas.read_csv(self.flye_assembly_info_file, header=0, index_col=0, sep='\t')
            # Look for non-circular contigs.
            open_contigs = assembly_info.loc[assembly_info['circ.'] == 'N', :]