comparison flexynesis_utils.py @ 2:3c5d82bf6e8a draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a

1:262c2132b392

    os.makedirs(os.path.join(output_dir, 'test'), exist_ok=True)

    # Save train and test data
    for key in data.keys():
        try:
            train_data[key].to_csv(os.path.join(output_dir, 'train', f'{key}.csv'))
            test_data[key].to_csv(os.path.join(output_dir, 'test', f'{key}.csv'))
        except Exception as e:
            print(f"Error saving {key}: {e}")
            continue

            if mutations_df.empty:
                raise ValueError("Mutation data file is empty")

            binarized_matrix = binarize_mutations(mutations_df, gene_idx=args.gene_idx, sample_idx=args.sample_idx)
            # Save binarized matrix
            output_file = os.path.join(args.out, 'binarized_mutations.csv')
            binarized_matrix.to_csv(output_file)
            print(f"Binarized mutation matrix saved to {output_file}")

    except Exception as e:
        print(f"Error: {e}", file=sys.stderr)
        sys.exit(1)

2:3c5d82bf6e8a

    os.makedirs(os.path.join(output_dir, 'test'), exist_ok=True)

    # Save train and test data
    for key in data.keys():
        try:
            train_data[key].to_csv(os.path.join(output_dir, 'train', f'{key}.tabular'), sep='\t')
            test_data[key].to_csv(os.path.join(output_dir, 'test', f'{key}.tabular'), sep='\t')
        except Exception as e:
            print(f"Error saving {key}: {e}")
            continue

            if mutations_df.empty:
                raise ValueError("Mutation data file is empty")

            binarized_matrix = binarize_mutations(mutations_df, gene_idx=args.gene_idx, sample_idx=args.sample_idx)
            # Save binarized matrix
            output_file = os.path.join(args.out, 'binarized_mutations.tabular')
            binarized_matrix.to_csv(output_file, sep='\t')
            print(f"Binarized mutation matrix saved to {output_file}")

    except Exception as e:
        print(f"Error: {e}", file=sys.stderr)
        sys.exit(1)