Mercurial > repos > greg > draw_amr_matrix
comparison draw_amr_matrix.py @ 16:7bd48449ee79 draft
Uploaded
author | greg |
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date | Mon, 01 May 2023 18:52:58 +0000 |
parents | 487a3c008812 |
children | eb86b4bf140e |
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15:487a3c008812 | 16:7bd48449ee79 |
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233 parser.add_argument('--amr_gene_drug_file', action='store', dest='amr_gene_drug_file', help='AMR_gene_drugs tsv file') | 233 parser.add_argument('--amr_gene_drug_file', action='store', dest='amr_gene_drug_file', help='AMR_gene_drugs tsv file') |
234 parser.add_argument('--reference_genome', action='store', dest='reference_genome', help='Reference genome fasta file') | 234 parser.add_argument('--reference_genome', action='store', dest='reference_genome', help='Reference genome fasta file') |
235 parser.add_argument('--mutation_regions_dir', action='store', dest='mutation_regions_dir', help='Directory for mutation regions TSV files produced by this tool') | 235 parser.add_argument('--mutation_regions_dir', action='store', dest='mutation_regions_dir', help='Directory for mutation regions TSV files produced by this tool') |
236 parser.add_argument('--amr_matrix_png_dir', action='store', dest='amr_matrix_png_dir', help='Directory for PNG files produced by this tool') | 236 parser.add_argument('--amr_matrix_png_dir', action='store', dest='amr_matrix_png_dir', help='Directory for PNG files produced by this tool') |
237 parser.add_argument('--errors', action='store', dest='errors', help='Output file containing errors') | 237 parser.add_argument('--errors', action='store', dest='errors', help='Output file containing errors') |
238 parser.add_argument('--in_test_mode', action='store', dest='in_test_mode', help='Flag for running functional tests') | |
239 | 238 |
240 args = parser.parse_args() | 239 args = parser.parse_args() |
241 | 240 |
242 # Get the collection of feature hits files. The collection | 241 # Get the collection of feature hits files. The collection |
243 # will be sorted alphabetically and will contain 2 files | 242 # will be sorted alphabetically and will contain 2 files |
252 reference = load_fasta(args.reference_genome) | 251 reference = load_fasta(args.reference_genome) |
253 reference_size = 0 | 252 reference_size = 0 |
254 for i in reference: | 253 for i in reference: |
255 reference_size += len(i.seq) | 254 reference_size += len(i.seq) |
256 | 255 |
257 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) | 256 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) |