comparison draw_amr_matrix.py @ 15:487a3c008812 draft

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14:c5e80637cf3d

def stop_err(msg):
    sys.stderr.write(msg)
    sys.exit(1)


def draw_amr_matrix(amr_feature_hits_files, amr_deletions_file, varscan_vcf_file, amr_mutation_regions_bed_file, amr_gene_drug_file, reference, reference_size, mutation_regions_dir, amr_matrix_png_dir, errors, in_test_mode):
    efh = open(errors, 'w')
    ofh = open('process_log', 'w')

    # Read amr_feature_hits_files.
    amr_feature_hits = pandas.Series(dtype=object)

                for deletion_idx, deleted_gene in amr_deletions.iterrows():
                    amr_to_draw = amr_to_draw.append(pandas.Series(['\u0394' + deleted_gene[3], deleted_gene[5]], name=amr_to_draw.shape[0], index=amr_to_draw.columns))
            ofh.write("\nAfter processing deletions, amr_to_draw: %s\n" % str(amr_to_draw))

        ofh.write("\namr_to_draw.shape[0]: %s\n" % str(amr_to_draw.shape[0]))
        # I have no idea why, but when running functional test with planemo
        # the value of amr_to_draw.shape[0] is 1 even though the tests use the
        # exact inputs when running outside of planeo that result in the value
        # being 2.  So we have to pass this in_test_mode flag in order to get
        # functional tests to work.
        if in_test_mode == 'true':
            shape_val = 0
        else:
            shape_val = 1
        if amr_to_draw.shape[0] > shape_val:
            ofh.write("\nDrawing AMR matrix...\n")
            present_genes = amr_to_draw['gene'].unique()
            present_drugs = amr_to_draw['drug'].unique()
            amr_matrix = pandas.DataFrame(0, index=present_genes, columns=present_drugs)
            for hit_idx, hit in amr_to_draw.iterrows():

15:487a3c008812

def stop_err(msg):
    sys.stderr.write(msg)
    sys.exit(1)


def draw_amr_matrix(amr_feature_hits_files, amr_deletions_file, varscan_vcf_file, amr_mutation_regions_bed_file, amr_gene_drug_file, reference, reference_size, mutation_regions_dir, amr_matrix_png_dir, errors):
    efh = open(errors, 'w')
    ofh = open('process_log', 'w')

    # Read amr_feature_hits_files.
    amr_feature_hits = pandas.Series(dtype=object)

                for deletion_idx, deleted_gene in amr_deletions.iterrows():
                    amr_to_draw = amr_to_draw.append(pandas.Series(['\u0394' + deleted_gene[3], deleted_gene[5]], name=amr_to_draw.shape[0], index=amr_to_draw.columns))
            ofh.write("\nAfter processing deletions, amr_to_draw: %s\n" % str(amr_to_draw))

        ofh.write("\namr_to_draw.shape[0]: %s\n" % str(amr_to_draw.shape[0]))
        # I have no idea why, but when running functional tests with planemo
        # the value of amr_to_draw.shape[0] is 1 even though the tests use the
        # exact inputs when running outside of planeo that result in the value
        # being 2.  So we cannot test with planemo unless we incorporate a hack
        # like a hidden in_test_mode parameter.
        if amr_to_draw.shape[0] > 1:
            ofh.write("\nDrawing AMR matrix...\n")
            present_genes = amr_to_draw['gene'].unique()
            present_drugs = amr_to_draw['drug'].unique()
            amr_matrix = pandas.DataFrame(0, index=present_genes, columns=present_drugs)
            for hit_idx, hit in amr_to_draw.iterrows():