comparison draw_amr_matrix.py @ 16:7bd48449ee79 draft

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15:487a3c008812

    parser.add_argument('--amr_gene_drug_file', action='store', dest='amr_gene_drug_file', help='AMR_gene_drugs tsv file')
    parser.add_argument('--reference_genome', action='store', dest='reference_genome', help='Reference genome fasta file')
    parser.add_argument('--mutation_regions_dir', action='store', dest='mutation_regions_dir', help='Directory for mutation regions TSV files produced by this tool')
    parser.add_argument('--amr_matrix_png_dir', action='store', dest='amr_matrix_png_dir', help='Directory for PNG files produced by this tool')
    parser.add_argument('--errors', action='store', dest='errors', help='Output file containing errors')
    parser.add_argument('--in_test_mode', action='store', dest='in_test_mode', help='Flag for running functional tests')

    args = parser.parse_args()

    # Get the collection of feature hits files.  The collection
    # will be sorted alphabetically and will contain 2 files

    reference = load_fasta(args.reference_genome)
    reference_size = 0
    for i in reference:
        reference_size += len(i.seq)

    draw_amr_matrix(amr_feature_hits_files, args.amr_deletions_file, args.varscan_vcf_file, args.amr_mutation_regions_bed_file, args.amr_gene_drug_file, reference, reference_size, args.mutation_regions_dir, args.amr_matrix_png_dir, args.errors, args.in_test_mode)

16:7bd48449ee79

    parser.add_argument('--amr_gene_drug_file', action='store', dest='amr_gene_drug_file', help='AMR_gene_drugs tsv file')
    parser.add_argument('--reference_genome', action='store', dest='reference_genome', help='Reference genome fasta file')
    parser.add_argument('--mutation_regions_dir', action='store', dest='mutation_regions_dir', help='Directory for mutation regions TSV files produced by this tool')
    parser.add_argument('--amr_matrix_png_dir', action='store', dest='amr_matrix_png_dir', help='Directory for PNG files produced by this tool')
    parser.add_argument('--errors', action='store', dest='errors', help='Output file containing errors')

    args = parser.parse_args()

    # Get the collection of feature hits files.  The collection
    # will be sorted alphabetically and will contain 2 files

    reference = load_fasta(args.reference_genome)
    reference_size = 0
    for i in reference:
        reference_size += len(i.seq)

    draw_amr_matrix(amr_feature_hits_files, args.amr_deletions_file, args.varscan_vcf_file, args.amr_mutation_regions_bed_file, args.amr_gene_drug_file, reference, reference_size, args.mutation_regions_dir, args.amr_matrix_png_dir, args.errors)