comparison draw_amr_matrix.py @ 6:caf554e039b2 draft

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5:46d31ec5d24c

                        ofh.write("\nFinding AMR mutations for %s.\n" % str(region['name']))
                        region_dir = os.path.join(mutations_dir, 'region_' + str(region_i))
                        os.mkdir(region_dir)
                        region_bed = os.path.join(region_dir, 'region.bed')
                        mutation_regions.loc[[region_i], ].to_csv(path_or_buf=region_bed, sep='\t', header=False, index=False)
                        cmd = "bedtools intersect -nonamecheck -wb -a '%s' -b '%s' | awk '{BEGIN{getline < \"%s\" ;printf $0\"\t\";getline < \"%s\"; getline < \"%s\";print $0}{print}' > %s" % (region_bed, amr_mutations_file, amr_mutation_regions_file, amr_mutations_file, amr_mutations_file, region_mutations_output_file)
                        run_command(cmd)
                        try:
                            region_mutations = pandas.read_csv(region_mutations_output_file, sep='\t', header=0, index_col=False)
                        except Exception:
                            region_mutations = pandas.DataFrame()

                for mutation_idx, mutation_hit in mutation_hits.iterrows():
                    mutation_name = mutation_region + ' ' + mutation_hit['REF'] + '->' + mutation_hit['ALT']
                    amr_to_draw = amr_to_draw.append(pandas.Series([mutation_name, mutation_hit['DRUG']], name=amr_to_draw.shape[0], index=amr_to_draw.columns))

        if amr_deletions_file not in [None, 'None'] and os.path.getsize(amr_deletions_file) > 0:
            # TODO: So far, no samples have produced deletions, but we do have all the pices in place
            # within the workflow to receive the amr_deletions_file here, although it is currently
            # always empty...
            # Roll up deletions that might confer resistance.
            try:
                amr_deletions = pandas.read_csv(filepath_or_buffer=amr_deletions_file, sep='\t', header=None)
            except Exception:
                amr_deletions = pandas.DataFrame()

            for hit_idx, hit in amr_to_draw.iterrows():
                amr_matrix.loc[hit[0], hit[1]] = 1
            amr_matrix_png = os.path.join(output_dir, 'amr_matrix.png')
            int_matrix = amr_matrix[amr_matrix.columns].astype(int)
            figure, axis = pyplot.subplots()
            axis.invert_yaxis()
            axis.set_yticks(numpy.arange(0.5, len(amr_matrix.index)), minor=False)
            axis.set_yticklabels(int_matrix.index.values)
            axis.set_xticks(numpy.arange(0.5, len(amr_matrix.columns)), minor=False)
            axis.set_xticklabels(amr_matrix.columns.values, rotation=90)

6:caf554e039b2

                        ofh.write("\nFinding AMR mutations for %s.\n" % str(region['name']))
                        region_dir = os.path.join(mutations_dir, 'region_' + str(region_i))
                        os.mkdir(region_dir)
                        region_bed = os.path.join(region_dir, 'region.bed')
                        mutation_regions.loc[[region_i], ].to_csv(path_or_buf=region_bed, sep='\t', header=False, index=False)
                        cmd = ' '.join(['bedtools intersect -nonamecheck -wb -a',
                                        region_bed,
                                        '-b',
                                        amr_mutations_file,
                                        ' | awk \'BEGIN{getline < "' + amr_mutation_regions_file + '";printf $0"\\t";',
                                        'getline < "' + amr_mutations_file + '"; getline < "' + amr_mutations_file + '";print $0}{print}\'',
                                        '1>' + region_mutations_output_file])
                        ofh.write("\ncmd:\n%s\n" % cmd)
                        run_command(cmd)
                        try:
                            region_mutations = pandas.read_csv(region_mutations_output_file, sep='\t', header=0, index_col=False)
                        except Exception:
                            region_mutations = pandas.DataFrame()

                for mutation_idx, mutation_hit in mutation_hits.iterrows():
                    mutation_name = mutation_region + ' ' + mutation_hit['REF'] + '->' + mutation_hit['ALT']
                    amr_to_draw = amr_to_draw.append(pandas.Series([mutation_name, mutation_hit['DRUG']], name=amr_to_draw.shape[0], index=amr_to_draw.columns))

        if amr_deletions_file not in [None, 'None'] and os.path.getsize(amr_deletions_file) > 0:
            # Roll up deletions that might confer resistance.
            try:
                amr_deletions = pandas.read_csv(filepath_or_buffer=amr_deletions_file, sep='\t', header=None)
            except Exception:
                amr_deletions = pandas.DataFrame()

            for hit_idx, hit in amr_to_draw.iterrows():
                amr_matrix.loc[hit[0], hit[1]] = 1
            amr_matrix_png = os.path.join(output_dir, 'amr_matrix.png')
            int_matrix = amr_matrix[amr_matrix.columns].astype(int)
            figure, axis = pyplot.subplots()
            heatmap = axis.pcolor(int_matrix, cmap=pyplot.cm.Blues, linewidth=0)
            axis.invert_yaxis()
            axis.set_yticks(numpy.arange(0.5, len(amr_matrix.index)), minor=False)
            axis.set_yticklabels(int_matrix.index.values)
            axis.set_xticks(numpy.arange(0.5, len(amr_matrix.columns)), minor=False)
            axis.set_xticklabels(amr_matrix.columns.values, rotation=90)