Mercurial > repos > greg > draw_amr_matrix
changeset 9:70073df30a06 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 21 Mar 2023 14:06:11 +0000 |
| parents | 7fe8ea50a81d |
| children | 03240ffe969a |
| files | all_fasta.loc.sample draw_amr_matrix.py draw_amr_matrix.xml test-data/amr_gene_drug.tsv tool-data/all_fasta.loc.sample |
| diffstat | 5 files changed, 44 insertions(+), 3128 deletions(-) [+] |
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--- a/all_fasta.loc.sample Wed Mar 15 13:31:18 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -#This file lists the locations and dbkeys of all the fasta files -#under the "genome" directory (a directory that contains a directory -#for each build). The script extract_fasta.py will generate the file -#all_fasta.loc. This file has the format (white space characters are -#TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_path> -# -#So, all_fasta.loc could look something like this: -# -#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa -# -#Your all_fasta.loc file should contain an entry for each individual -#fasta file. So there will be multiple fasta files for each build, -#such as with hg19 above. -#
--- a/draw_amr_matrix.py Wed Mar 15 13:31:18 2023 +0000 +++ b/draw_amr_matrix.py Tue Mar 21 14:06:11 2023 +0000 @@ -58,7 +58,8 @@ 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): +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. @@ -98,19 +99,34 @@ amr_to_draw = amr_to_draw.append(pandas.Series([gene_name, drug], name=amr_to_draw.shape[0], index=amr_to_draw.columns)) ofh.write("\amr_to_draw: %s\n" % str(amr_to_draw)) - ofh.write("\nvarscan_vcf_file si None: %s\n" % str(varscan_vcf_file == 'None')) + ofh.write("\nvarscan_vcf_file is None: %s\n" % str(varscan_vcf_file == 'None')) if varscan_vcf_file not in [None, 'None'] and os.path.getsize(varscan_vcf_file) > 0: amr_mutations = pandas.Series(dtype=object) if amr_mutation_regions_bed_file is not None: mutation_regions = pandas.read_csv(amr_mutation_regions_bed_file, header=0, sep='\t', index_col=False) + # Validate mutation regions. if mutation_regions.shape[1] != 7: - ofh.write("\nMutation regions should be a six column file.\n") + efh.write("\nThe selected mutations regions BED file is invalid, it should be a six column file.\n") elif mutation_regions.shape[0] == 0: - ofh.write("\nNo rows in mutation regions file.\n") + efh.write("\nThere are no rows in the selected mutation regions file.\n") else: for region_i in range(mutation_regions.shape[0]): region = mutation_regions.iloc[region_i, :] + if region[0] not in reference: + efh.write("\nMutation region '%s' not found in reference genome.\n" % str(region)) + break + if not isinstance(region[1], numpy.int64): + efh.write("\nNon-integer found in mutation region start (column 2): %s.\n" % str(region[1])) + break + if not isinstance(region[2], numpy.int64): + efh.write("\nNon-integer found in mutation region start (column 3): %s.\n" % str(region[2])) + break + if region[1] <= 0 or region[2] <= 0: + efh.write("\nMutation region '%s' starts before the reference sequence.\n" % str(region)) + if region[1] > len(reference[region[0]].seq) or region[2] > len(reference[region[0]].seq): + efh.write("\nMutation region '%s' ends after the reference sequence.\n" % str(region)) if not region.get('type', default='No Type') in ['snp', 'small-indel', 'any']: + ofh.write("\n\nSkipping mutation region '%s' with invalid type '%s', valid types are 'snp', 'small-indel', 'any'.\n\n" % (str(region), str(region.get('type', default='No Type')))) continue ofh.write("\nFinding AMR mutations for %s.\n" % str(region['name'])) region_bed = 'region_%s.bed' % region_i @@ -167,6 +183,7 @@ pyplot.savefig(amr_matrix_png, dpi=300) else: ofh.write("\nEmpty AMR matrix, nothing to draw...\n") + efh.close() ofh.close() @@ -181,6 +198,7 @@ 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() @@ -199,4 +217,4 @@ 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) + 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)
--- a/draw_amr_matrix.xml Wed Mar 15 13:31:18 2023 +0000 +++ b/draw_amr_matrix.xml Tue Mar 21 14:06:11 2023 +0000 @@ -38,6 +38,7 @@ --amr_gene_drug_file '$amr_gene_drug_file' --reference_genome reference.fa --amr_matrix_png_dir 'amr_matrix_png_dir' +--errors '$errors' #if str($output_process_log) == 'yes': && mv 'process_log' '$process_log' #end if @@ -74,6 +75,7 @@ <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)"> <filter>output_process_log == 'yes'</filter> </data> + <data name="errors" format="txt" label="${tool.name} on ${on_string} (errors)"/> <collection name="mutation_regions_tsv" type="list" format="tsv" label="${tool.name} on ${on_string} (mutation regions)"> <filter>amr_mutation_regions_bed_file not in [None, 'None']</filter> <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>tsv)" directory="mutation_regions_dir"/> @@ -99,6 +101,7 @@ </assert_contents> </element> </output_collection> + <output name="errors" value="errors.txt" ftype="txt"/> </test> </tests> <help>
--- a/test-data/amr_gene_drug.tsv Wed Mar 15 13:31:18 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3105 +0,0 @@ -aac(6')-Ib_2 aminoglycoside -aac(6')-Ib11_1 aminoglycoside -aac(6')-30-aac(6')-Ib'_1 aminoglycoside -aac(6')-Iaj_1 aminoglycoside -aac(6')-Ian_1 aminoglycoside -aac(6')-Iak_1 aminoglycoside -aac(6')-Ib-Hangzhou_1 aminoglycoside -aac(6')-Ib-Suzhou_1 aminoglycoside -aac(6')-Iid_1 aminoglycoside -aac(6')-Iih_1 aminoglycoside -aac(6')-Iz_2 aminoglycoside -aac(6')-29b_1 aminoglycoside -aac(6')-29a_1 aminoglycoside -aac(6')-Iaa_1 aminoglycoside -aac(6')-Ih_2 aminoglycoside -aac(6')-Ix_1 aminoglycoside -aac(6')-Il_1 aminoglycoside -aac(6')-Ia_2 aminoglycoside -aac(6')-Iag_1 aminoglycoside -aac(2')-IIa_1 aminoglycoside -kamB_1 aminoglycoside -grmO_1 aminoglycoside -fmrO_1 aminoglycoside -grmB_1 aminoglycoside -grmA_1 aminoglycoside -kgmB_1 aminoglycoside -sgm_1 aminoglycoside -aph(3')-VI_2 aminoglycoside -aph(3')-IX_1 aminoglycoside -ant(6)-Ia_5 aminoglycoside -aadA13_2 aminoglycoside -aadA11_2 aminoglycoside -aadA10_2 aminoglycoside -aadA7_2 aminoglycoside -aadA2_1 aminoglycoside -aadD_2 aminoglycoside -aph(2'')-Ib_2 aminoglycoside -aph(7'')-Ia_1 aminoglycoside -aph(9)-Ia_2 aminoglycoside -aph(6)-Ia_2 aminoglycoside -aph(6)-Id_1 aminoglycoside -aph(6)-Id_3 aminoglycoside -aph(6)-Id_4 aminoglycoside -aph(6)-Id_5 aminoglycoside -aph(3'')-Ia_2 aminoglycoside -aph(3'')-Ia_3 aminoglycoside -aph(3'')-Ib_1 aminoglycoside -aph(3'')-Ib_3 aminoglycoside -aph(3'')-Ib_4 aminoglycoside -aadE-Cc_1 aminoglycoside -ant(2'')-Ia_2 aminoglycoside -ant(2'')-Ia_3 aminoglycoside -ant(2'')-Ia_4 aminoglycoside -ant(2'')-Ia_5 aminoglycoside -ant(2'')-Ia_6 aminoglycoside -ant(2'')-Ia_7 aminoglycoside -ant(2'')-Ia_8 aminoglycoside -ant(2'')-Ia_9 aminoglycoside -ant(2'')-Ia_10 aminoglycoside -ant(2'')-Ia_11 aminoglycoside -ant(2'')-Ia_12 aminoglycoside -ant(2'')-Ia_13 aminoglycoside -ant(2'')-Ia_14 aminoglycoside -ant(2'')-Ia_15 aminoglycoside -ant(2'')-Ia_16 aminoglycoside -ant(2'')-Ia_17 aminoglycoside -ant(2'')-Ia_19 aminoglycoside -ant(2'')-Ia_20 aminoglycoside -ant(2'')-Ia_1 aminoglycoside -aph(3')-VI_1 aminoglycoside -aph(3')-XV_2 aminoglycoside -aph(3')-XV_3 aminoglycoside -aph(3')-IIIa_1 aminoglycoside -aph(3')-IIIa_2 aminoglycoside -aph(3')-IIIa_3 aminoglycoside -aph(3')-Va_2 aminoglycoside -aph(3')-Vb_2 aminoglycoside -aph(3')-IIa_2 aminoglycoside -aph(3')-IIb_2 aminoglycoside -aph(3')-Ia_2 aminoglycoside -aph(3')-Ia_3 aminoglycoside -aph(3')-Ia_4 aminoglycoside -aph(3')-Ia_5 aminoglycoside -aph(3')-Ia_6 aminoglycoside -aph(3')-Ia_7 aminoglycoside -aph(3')-Ia_8 aminoglycoside -aph(3')-Ia_9 aminoglycoside -aph(3')-Ia_10 aminoglycoside -aph(2'')-Ih_1 aminoglycoside -aph(2'')-Ig_1 aminoglycoside -aph(2'')-If_1 aminoglycoside -aph(2'')-If_2 aminoglycoside -aph(2'')-Ia_2 aminoglycoside -aph(2'')-Ia_3 aminoglycoside -aph(2'')-Ib_3 aminoglycoside -ant(6)-Ia_3 aminoglycoside -aac(2')-Ia_1 aminoglycoside -aac(2')-Ib_1 aminoglycoside -aac(2')-Ic_1 aminoglycoside -aac(2')-Id_1 aminoglycoside -aac(2')-Ie_1 aminoglycoside -aac(3)-I_1 aminoglycoside -aac(3)-Ia_1 aminoglycoside -aac(3)-Ib_1 aminoglycoside -aac(3)-Ib-aac(6')-Ib'_1 aminoglycoside -aac(3)-Ic_1 aminoglycoside -aac(3)-Id_1 aminoglycoside -aac(3)-If_1 aminoglycoside -aac(3)-Ig_1 aminoglycoside -aac(3)-Ih_1 aminoglycoside -aac(3)-Ii_1 aminoglycoside -aac(3)-IIa_1 aminoglycoside -aac(3)-IIb_1 aminoglycoside -aac(3)-IIc_1 aminoglycoside -aac(3)-IId_1 aminoglycoside -aac(3)-IIe_1 aminoglycoside -aac(3)-IIIa_1 aminoglycoside -aac(3)-IIIb_1 aminoglycoside -aac(3)-IIIc_1 aminoglycoside -aac(3)-IVa_1 aminoglycoside -aac(3)-VIa_1 aminoglycoside -aac(3)-VIIa_1 aminoglycoside -aac(3)-VIIIa_1 aminoglycoside -aac(3)-IXa_1 aminoglycoside -aac(3)-Xa_1 aminoglycoside -aac(6')-Ia_1 aminoglycoside -aac(6')-Ib_1 aminoglycoside -aac(6')-Ic_1 aminoglycoside -aac(6')-If_1 aminoglycoside -aac(6')-Ig_1 aminoglycoside -aac(6')-Ih_1 aminoglycoside -aac(6')-Ij_1 aminoglycoside -aac(6')-Ik_1 aminoglycoside -aac(6')-Ip_1 aminoglycoside -aac(6')-Im_1 aminoglycoside -aac(6')-Iq_1 aminoglycoside -aac(6')-Ir_1 aminoglycoside -aac(6')-Is_1 aminoglycoside -aac(6')-It_1 aminoglycoside -aac(6')-Iu_1 aminoglycoside -aac(6')-Iv_1 aminoglycoside -aac(6')-Iw_1 aminoglycoside -aac(6')-Iz_1 aminoglycoside -aac(6')-Iad_1 aminoglycoside -aac(6')-Iae_1 aminoglycoside -aac(6')-Iaf_1 aminoglycoside -aac(6')-Iai_1 aminoglycoside -aac(6')-I30_1 aminoglycoside -aac(6')-31_1 aminoglycoside -aac(6')-32_1 aminoglycoside -aac(6')-33_1 aminoglycoside -aac(6')-IIa_1 aminoglycoside -aac(6')-IIb_1 aminoglycoside -aac(6')-IIc_1 aminoglycoside -aac(6')-aph(2'')_1 aminoglycoside -aac(6')-Isa_1 aminoglycoside -aac(6')-Ib3_1 aminoglycoside -aacA43_1 aminoglycoside -ant(3'')-Ia_1 aminoglycoside -aadA1_2 aminoglycoside -aadA1_3 aminoglycoside -aadA1b_1 aminoglycoside -aadA1_4 aminoglycoside -aadA1_5 aminoglycoside -aadA2_2 aminoglycoside -aadA3_1 aminoglycoside -aadA4_1 aminoglycoside -aadA5_1 aminoglycoside -aadA6_1 aminoglycoside -aadA7_1 aminoglycoside -aadA8_1 aminoglycoside -aadA8b_2 aminoglycoside -aadA9_1 aminoglycoside -aadA10_1 aminoglycoside -aadA11_1 aminoglycoside -aadA12_1 aminoglycoside -aadA13_1 aminoglycoside -aadA14_1 aminoglycoside -aadA15_1 aminoglycoside -aadA16_1 aminoglycoside -aadA17_1 aminoglycoside -aadA21_1 aminoglycoside -aadA22_1 aminoglycoside -aadA23_1 aminoglycoside -aadA24_1 aminoglycoside -ant(6)-Ia_2 aminoglycoside -aadD_1 aminoglycoside -aadK_1 aminoglycoside -ant(3'')-Ii-aac(6')-IId_1 aminoglycoside -ant(4')-Ib_1 aminoglycoside -ant(4')-IIa_1 aminoglycoside -ant(4')-IIb_1 aminoglycoside -ant(6)-Ia_1 aminoglycoside -ant(6)-Ib_1 aminoglycoside -aph(2'')-Ib_1 aminoglycoside -aph(2'')-Ic_1 aminoglycoside -aph(2'')-Id_1 aminoglycoside -aph(2'')-Ie_1 aminoglycoside -aph(3')-Ia_1 aminoglycoside -aph(3')-Ib_1 aminoglycoside -aph(3'')-Ic_1 aminoglycoside -aph(3')-Id_1 aminoglycoside -aph(3')-IIa_1 aminoglycoside -aph(3')-IIb_1 aminoglycoside -aph(3')-IIc_1 aminoglycoside -aph(3')-III_1 aminoglycoside -aph(3')-IV_1 aminoglycoside -aph(3')-Va_1 aminoglycoside -aph(3')-Vb_1 aminoglycoside -aph(3')-Vc_1 aminoglycoside -aph(3')-VIa_1 aminoglycoside -aph(3')-VIb_1 aminoglycoside -aph(3')-VIIa_1 aminoglycoside -aph(3')-VIII_1 aminoglycoside -aph(3')-XV_1 aminoglycoside -aph(3'')-Ia_1 aminoglycoside -aph(4)-Ia_1 aminoglycoside -aph(6)-Ia_1 aminoglycoside -aph(6)-Ib_1 aminoglycoside -aph(6)-Ic_1 aminoglycoside -aph(9)-Ia_1 aminoglycoside -aph(9)-Ib_1 aminoglycoside -rmtB2_1 aminoglycoside -rmtF_1 aminoglycoside -rmtG_1 aminoglycoside -rmtH_1 aminoglycoside -armA_1 aminoglycoside -npmA_1 aminoglycoside -rmtA_1 aminoglycoside -rmtB_1 aminoglycoside -rmtC_1 aminoglycoside -rmtD_1 aminoglycoside -rmtD2_1 aminoglycoside -rmtE_1 aminoglycoside -ant(9)-Ia_1 aminoglycoside -aac(6')-Ib-cr_1 aminoglycoside -aac(6')-Ib-cr_2 aminoglycoside -aph(3'')-Ib_2 aminoglycoside -aph(3'')-Ib_5 aminoglycoside -aph(6)-Id_2 aminoglycoside -str_1 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beta-lactam -blaOXA-362_1 beta-lactam -blaOXA-363_1 beta-lactam -blaOXA-364_1 beta-lactam -blaOXA-365_1 beta-lactam -blaOXA-366_1 beta-lactam -blaOXA-370_1 beta-lactam -blaOXA-373_1 beta-lactam -blaOXA-374_1 beta-lactam -blaOXA-375_1 beta-lactam -blaOXA-376_1 beta-lactam -blaOXA-377_1 beta-lactam -blaOXA-378_1 beta-lactam -blaOXA-379_1 beta-lactam -blaOXA-380_1 beta-lactam -blaOXA-381_1 beta-lactam -blaOXA-382_1 beta-lactam -blaOXA-383_1 beta-lactam -blaOXA-384_1 beta-lactam -blaOXA-385_1 beta-lactam -blaOXA-386_1 beta-lactam -blaOXA-387_1 beta-lactam -blaOXA-388_1 beta-lactam -blaOXA-389_1 beta-lactam -blaOXA-390_1 beta-lactam -blaOXA-391_1 beta-lactam -blaOXA-392_1 beta-lactam -blaOXA-395_1 beta-lactam -blaOXA-396_1 beta-lactam -blaOXA-397_1 beta-lactam -blaOXA-398_1 beta-lactam -blaOXA-400_1 beta-lactam -blaOXA-401_1 beta-lactam -blaOXA-402_1 beta-lactam -blaOXA-403_1 beta-lactam -blaOXA-404_1 beta-lactam -blaOXA-405_1 beta-lactam -blaOXA-406_1 beta-lactam -blaOXA-407_1 beta-lactam -blaOXA-408_1 beta-lactam -blaOXA-409_1 beta-lactam -blaOXA-410_1 beta-lactam -blaOXA-411_1 beta-lactam -blaOXA-412_1 beta-lactam -blaOXA-413_1 beta-lactam -blaOXA-414_1 beta-lactam -blaOXA-415_1 beta-lactam -blaOXA-416_1 beta-lactam -blaOXA-417_1 beta-lactam -blaOXA-418_1 beta-lactam -blaOXA-420_1 beta-lactam -blaOXA-421_1 beta-lactam -blaOXA-422_1 beta-lactam -blaOXA-423_1 beta-lactam -blaOXA-424_1 beta-lactam -blaOXA-425_1 beta-lactam -blaOXA-426_1 beta-lactam -blaOXA-429_1 beta-lactam -blaOXA-430_1 beta-lactam -blaOXA-431_1 beta-lactam -blaOXA-432_1 beta-lactam -blaOXA-433_1 beta-lactam -blaOXA-435_1 beta-lactam -blaOXA-436_1 beta-lactam -blaOXA-437_1 beta-lactam -blaOXA-438_1 beta-lactam -blaOXA-439_1 beta-lactam -blaOXA-440_1 beta-lactam -blaOXA-441_1 beta-lactam -blaOXA-442_1 beta-lactam -blaOXA-443_1 beta-lactam -blaOXA-444_1 beta-lactam -blaOXA-450_1 beta-lactam -blaOXA-451_1 beta-lactam -blaOXA-452_1 beta-lactam -blaOXA-453_1 beta-lactam -blaOXA-454_1 beta-lactam 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-blaTEM-19_1 beta-lactam -blaTEM-9_1 beta-lactam -blaTEM-4_1 beta-lactam -blaTEM-169_1 beta-lactam -blaTEM-144_1 beta-lactam -blaTEM-129_1 beta-lactam -blaTEM-128_1 beta-lactam -blaTEM-181_1 beta-lactam -blaTEM-191_1 beta-lactam -blaTEM-196_1 beta-lactam -blaTEM-210_1 beta-lactam -blaTEM-212_1 beta-lactam -blaTEM-213_1 beta-lactam -blaTEM-214_1 beta-lactam -blaTEM-215_1 beta-lactam -blaTEM-216_1 beta-lactam -blaTEM-217_1 beta-lactam -blaTEM-219_1 beta-lactam -blaTEM-220_1 beta-lactam -blaTEM-224_1 beta-lactam -blaTEM-225_1 beta-lactam -blaTEM-226_1 beta-lactam -blaTEM-227_1 beta-lactam -blaTEM-229_1 beta-lactam -blaTEM-230_1 beta-lactam -blaTEM-231_1 beta-lactam -blaTEM-232_1 beta-lactam -blaTEM-233_1 beta-lactam -blaTEM-234_1 beta-lactam -blaSHV-1_1 beta-lactam -blaSHV-2_1 beta-lactam -blaSHV-3_1 beta-lactam -blaSHV-9_1 beta-lactam -blaSHV-11_1 beta-lactam -blaSHV-12_1 beta-lactam -blaSHV-32_1 beta-lactam -blaSHV-36_2 beta-lactam -blaSHV-38_1 beta-lactam -blaSHV-42_1 beta-lactam -blaSHV-71_1 beta-lactam -blaSHV-111_1 beta-lactam -blaSHV-119_1 beta-lactam -blaSHV-189_1 beta-lactam -blaSHV-188_1 beta-lactam -blaSHV-187_1 beta-lactam -blaSHV-186_1 beta-lactam -blaSHV-185_1 beta-lactam -blaSHV-183_1 beta-lactam -blaSHV-182_1 beta-lactam -blaSHV-180_1 beta-lactam -blaSHV-190_1 beta-lactam -blaSHV-191_1 beta-lactam -blaSHV-193_1 beta-lactam -blaSHV-194_1 beta-lactam -blaSHV-195_1 beta-lactam -blaSHV-196_1 beta-lactam -blaSHV-197_1 beta-lactam -blaSHV-198_1 beta-lactam -blaSHV-199_1 beta-lactam -blaSHV-200_1 beta-lactam -blaSHV-203_1 beta-lactam -blaSHV-204_1 beta-lactam -blaSHV-1b-b_1 beta-lactam -blaIMP-64_1 beta-lactam -blaOXA-20_2 beta-lactam -blaOXA-60d_1 beta-lactam -blaOXA-60c_1 beta-lactam -blaOXA-60b_1 beta-lactam -blaOXA-60a_1 beta-lactam -blaCARB-1_1 beta-lactam -blaCARB-2_1 beta-lactam -blaCARB-3_1 beta-lactam -blaCARB-4_1 beta-lactam -blaCARB-5_1 beta-lactam -blaCARB-6_1 beta-lactam -blaCARB-7_1 beta-lactam -blaCARB-8_1 beta-lactam -blaCARB-9_1 beta-lactam -blaCARB-10_1 beta-lactam -blaCARB-11_1 beta-lactam -blaCARB-12_1 beta-lactam -blaCARB-14_1 beta-lactam -blaCARB-16_1 beta-lactam -blaCARB-17_1 beta-lactam -blaCARB-18_1 beta-lactam -blaCARB-19_1 beta-lactam -blaCARB-20_1 beta-lactam -blaCARB-21_1 beta-lactam -blaCARB-22_1 beta-lactam -blaCARB-23_1 beta-lactam -blaCARB-24_1 beta-lactam -blaCARB-25_1 beta-lactam -blaCARB-26_1 beta-lactam -blaCARB-27_1 beta-lactam -blaCARB-28_1 beta-lactam -blaCARB-29_1 beta-lactam -blaCARB-30_1 beta-lactam -blaCARB-31_1 beta-lactam -blaCARB-32_1 beta-lactam -blaCARB-33_1 beta-lactam -blaCARB-34_1 beta-lactam -blaCARB-35_1 beta-lactam -blaCARB-36_1 beta-lactam -blaCARB-38_1 beta-lactam -blaCARB-40_1 beta-lactam -blaCARB-41_1 beta-lactam -blaCARB-42_1 beta-lactam -blaCARB-43_1 beta-lactam -blaCARB-44_1 beta-lactam -blaCARB-45_1 beta-lactam -blaCARB-46_1 beta-lactam -blaCARB-47_1 beta-lactam -blaCARB-48_1 beta-lactam -blaCARB-49_1 beta-lactam -blaCARB-50_1 beta-lactam -blaFRI-1_2 beta-lactam -blaFRI-2_1 beta-lactam -blaFRI-3_1 beta-lactam -blaFRI-4_1 beta-lactam -blaFRI-5_1 beta-lactam -blaLAP-1_1 beta-lactam -blaLAP-2_1 beta-lactam -mcr-1.1_1 colistin -mcr-1.2_1 colistin -mcr-1.3_1 colistin -mcr-1.4_1 colistin -mcr-1.5_1 colistin -mcr-1.6_1 colistin -mcr-1.7_1 colistin -mcr-1.8_1 colistin -mcr-1.9_1 colistin -mcr-1.10_1 colistin -mcr-1.11_1 colistin -mcr-1.12_1 colistin -mcr-1.13_1 colistin -mcr-1.14_1 colistin -mcr-2.1_1 colistin -mcr-2.2_1 colistin -mcr-3.1_1 colistin -mcr-3.2_1 colistin -mcr-3.3_1 colistin -mcr-3.4_1 colistin -mcr-3.5_1 colistin -mcr-3.6_1 colistin -mcr-3.7_1 colistin -mcr-3.8_1 colistin -mcr-3.9_1 colistin -mcr-3.10_1 colistin -mcr-3.11_1 colistin -mcr-3.12_1 colistin -mcr-3.13_1 colistin -mcr-3.14_1 colistin -mcr-3.15_1 colistin -mcr-3.16_1 colistin -mcr-3.17_1 colistin -mcr-3.18_1 colistin -mcr-3.19_1 colistin -mcr-3.20_1 colistin -mcr-3.21_1 colistin -mcr-3.22_1 colistin -mcr-3.23_1 colistin -mcr-3.24_1 colistin -mcr-3.25_1 colistin -mcr-4.1_1 colistin -mcr-4.2_1 colistin -mcr-4.3_1 colistin -mcr-4.6_1 colistin -mcr-4.4_1 colistin -mcr-4.5_1 colistin -mcr-5.1_1 colistin -mcr-5.2_1 colistin -mcr-6.1_1 colistin -mcr-7.1_1 colistin -mcr-8_1 colistin -mcr-9_1 colistin -fosB1_1 fosfomycin -fosX_1 fosfomycin -fos_1 fosfomycin -fosB3_1 fosfomycin -fosB2_1 fosfomycin -fosB_1 fosfomycin -fosB_2 fosfomycin -fosA5_1 fosfomycin -fosA4_1 fosfomycin -fosA3_1 fosfomycin -fosA2_1 fosfomycin -fosA_1 fosfomycin -fosX_2 fosfomycin -fosK_1 fosfomycin -fosX_3 fosfomycin -fosX_4 fosfomycin -fosG_1 fosfomycin -fosF_1 fosfomycin -fosE_1 fosfomycin -fosD_1 fosfomycin -fosC2_1 fosfomycin -fosC_1 fosfomycin -fosB_3 fosfomycin -fosB_4 fosfomycin -fosB_5 fosfomycin -fosA_3 fosfomycin -fosA_4 fosfomycin -fosA_5 fosfomycin -fomB_1 fosfomycin -fomA_1 fosfomycin -fos_2 fosfomycin -fosE_2 fosfomycin -fosA7_1 fosfomycin -fosB5_1 fosfomycin -fosB6_1 fosfomycin -fosB4_1 fosfomycin -fosA_7 fosfomycin -fosA_2 fosfomycin -fosA6_1 fosfomycin -fosA_6 fosfomycin -fusB_1 fusidicacid -fusB_2 fusidicacid -fusC_1 fusidicacid -VanHAX_1 glycopeptide -VanHAX_2 glycopeptide -VanHAX_PT_1 glycopeptide -VanHAX_PA_1 glycopeptide -VanHAX_PT_2 glycopeptide -VanH_bc_1 glycopeptide -VanA_bc_1 glycopeptide -VanX_bc_1 glycopeptide -dldHA2X_1 glycopeptide -VanHBX_1 glycopeptide -VanHBX_2 glycopeptide -VanC1XY_1 glycopeptide -VanXY_C2_1 glycopeptide -VanC2_1 glycopeptide -VanC3XY_1 glycopeptide -VanC1XY_2 glycopeptide -VanC2XY_1 glycopeptide -VanC4XY_1 glycopeptide -VanC4XY_2 glycopeptide -VanC2XY_2 glycopeptide -VanC4XY_3 glycopeptide -VanC2XY_3 glycopeptide -VanC2XY_4 glycopeptide -VanC3XY_2 glycopeptide -VanC2XY_5 glycopeptide -VanHDX_6 glycopeptide -VanHDX_7 glycopeptide -VanHDX_3 glycopeptide -VanHDX_4 glycopeptide -VanHDX_5 glycopeptide -VanHDX_1 glycopeptide -VanHDX_2 glycopeptide -VanHFX_1 glycopeptide -VanE_1 glycopeptide -VanEXY_1 glycopeptide -VanGXY_1 glycopeptide -VanG2XY_1 glycopeptide -VanLXY_1 glycopeptide -VanHMX_1 glycopeptide -VanNXY_1 glycopeptide -VanHOX_1 glycopeptide -vanXmurFvanWI_1 glycopeptide -vanXmurFvanKWI_1 glycopeptide -vanXmurFvanKWI_2 glycopeptide -ere(A)_6 macrolide -ere(D)_1 macrolide -erm(A)_1 macrolide -erm(A)_2 macrolide -erm(A)_3 macrolide -erm(B)_1 macrolide -erm(B)_2 macrolide -erm(B)_6 macrolide -erm(B)_7 macrolide -erm(B)_9 macrolide -erm(B)_10 macrolide -erm(B)_11 macrolide -erm(B)_12 macrolide -erm(B)_15 macrolide -erm(B)_18 macrolide -erm(B)_20 macrolide -erm(B)_21 macrolide -erm(C)_1 macrolide -erm(C)_2 macrolide -erm(C)_3 macrolide -erm(C)_9 macrolide -erm(C)_10 macrolide -erm(C)_12 macrolide -erm(C)_13 macrolide -erm(C)_14 macrolide -erm(C)_15 macrolide -erm(C)_16 macrolide -erm(D)_1 macrolide -erm(D)_2 macrolide -erm(D)_3 macrolide -erm(E)_1 macrolide -erm(E)_2 macrolide -erm(F)_3 macrolide -erm(F)_4 macrolide -erm(G)_1 macrolide -erm(G)_2 macrolide -erm(H)_1 macrolide -erm(N)_1 macrolide -erm(O)_1 macrolide -erm(O)_2 macrolide -erm(Q)_1 macrolide -erm(S)_1 macrolide -erm(T)_1 macrolide -erm(T)_2 macrolide -erm(T)_3 macrolide -erm(T)_4 macrolide -erm(V)_1 macrolide -erm(X)_1 macrolide -erm(X)_2 macrolide -erm(X)_3 macrolide -erm(X)_4 macrolide -erm(Y)_1 macrolide -erm(Z)_1 macrolide -erm(30)_1 macrolide -erm(31)_1 macrolide -erm(32)_1 macrolide -erm(34)_1 macrolide -erm(35)_1 macrolide -erm(36)_1 macrolide -erm(38)_1 macrolide -erm(39)_1 macrolide -erm(40)_1 macrolide -erm(41)_1 macrolide -erm(42)_1 macrolide -erm(42)_2 macrolide -mef(A)_3 macrolide -mef(A)_4 macrolide -mef(B)_1 macrolide -msr(A)_1 macrolide -msr(A)_2 macrolide -msr(C)_1 macrolide -msr(C)_2 macrolide -msr(D)_2 macrolide -msr(D)_3 macrolide -msr(E)_1 macrolide -car(A)_1 macrolide -lmr(A)_1 macrolide -ole(B)_1 macrolide -ole(C)_1 macrolide -srm(B)_1 macrolide -tlr(C)_1 macrolide -lsa(B)_1 macrolide -lsa(C)_1 macrolide -vga(A)_1 macrolide -vga(A)_2 macrolide -vga(A)LC_3 macrolide -vga(A)LC_1 macrolide -vga(B)_1 macrolide -ere(A)_2 macrolide -ere(A)_3 macrolide -ere(A)_4 macrolide -ere(A)_1 macrolide -ere(B)_2 macrolide -vgb(A)_1 macrolide -vgb(B)_1 macrolide -lnu(A)_1 macrolide -lnu(B)_1 macrolide -lnu(C)_1 macrolide -lnu(D)_1 macrolide -lnu(F)_1 macrolide -lnu(F)_2 macrolide -lnu(F)_3 macrolide -vat(A)_1 macrolide -vat(B)_1 macrolide -vat(C)_1 macrolide -vat(D)_1 macrolide -vat(E)_3 macrolide -vat(E)_5 macrolide -vat(E)_7 macrolide -vat(E)_8 macrolide -vat(E)_9 macrolide -vat(E)_10 macrolide -vat(E)_11 macrolide -vat(F)_1 macrolide -mph(A)_1 macrolide -mph(A)_2 macrolide -mph(B)_1 macrolide -mph(C)_1 macrolide -mph(C)_2 macrolide -mph(C)_3 macrolide -mph(C)_4 macrolide -mph(C)_5 macrolide -mph(D)_1 macrolide -mph(E)_1 macrolide -mph(E)_2 macrolide -vga(D)_1 macrolide -vga(C)_1 macrolide -vga(E)_1 macrolide -lsa(A)_1 macrolide -lsa(A)_3 macrolide -erm(W)_1 macrolide -cfr_1 macrolide -cfr_2 macrolide -erm(48)_1 macrolide -mph(F)_1 macrolide -erm(46)_1 macrolide -erm(B)_22 macrolide -lnu(P)_1 macrolide -erm(43)_1 macrolide -mef(C)_1 macrolide -erm(47)_1 macrolide -erm(B)_26 macrolide -mph(G)_1 macrolide -lnu(G)_1 macrolide -mef(A)_1 macrolide -mef(A)_2 macrolide -vga(A)LC_2 macrolide -erm(44)v_1 macrolide -ere(B)_1 macrolide -erm(44)_1 macrolide -sal(A)_1 macrolide -erm(45)_1 macrolide -erm(33)_1 macrolide -ere(A)_5 macrolide -lnu(B)_2 macrolide -erm(R)_1 macrolide -erm(B)_23 macrolide -lnu(E)_1 macrolide -vat(H)_1 macrolide -erm(F)_1 macrolide -erm(37)_1 macrolide -vga(A)_3 macrolide -vga(A)V_1 macrolide -vga(A)LC_4 macrolide -tva(A)_1 macrolide -mph(N)_1 macrolide -mph(I)_1 macrolide -mph(J)_1 macrolide -mdf(A)_1 macrolide -mdt(A)_1 macrolide -mre(A)_1 macrolide -cmr_1 macrolide -erm(U)_1 macrolide -lsa(E)_1 macrolide -mph(K)_1 macrolide -nimA_1 nitroimidazole -nimB_1 nitroimidazole -nimC_1 nitroimidazole -nimD_1 nitroimidazole -nimE_1 nitroimidazole -nimE_2 nitroimidazole -nimF_1 nitroimidazole -nimH_1 nitroimidazole -nimI_1 nitroimidazole -nimI_2 nitroimidazole -nimI_3 nitroimidazole -nimI_4 nitroimidazole -nimI_5 nitroimidazole -nimJ_1 nitroimidazole -cfr_1 oxazolidinone -cfr_2 oxazolidinone -optrA_1 oxazolidinone -optrA_2 oxazolidinone -optrA_3 oxazolidinone -optrA_4 oxazolidinone -optrA_5 oxazolidinone -optrA_6 oxazolidinone -optrA_7 oxazolidinone -optrA_8 oxazolidinone -optrA_9 oxazolidinone -optrA_10 oxazolidinone -optrA_11 oxazolidinone -optrA_12 oxazolidinone -optrA_13 oxazolidinone -optrA_14 oxazolidinone -optrA_15 oxazolidinone -optrA_16 oxazolidinone -optrA_17 oxazolidinone -optrA_18 oxazolidinone -optrA_19 oxazolidinone -optrA_20 oxazolidinone -cfr(B)_3 oxazolidinone -poxtA_1 oxazolidinone -catB3_2 phenicol -catB_1 phenicol -catB1_1 phenicol -catB2_1 phenicol -catB3_1 phenicol -catB7_1 phenicol -catB8_1 phenicol -catB9_1 phenicol -catB10_1 phenicol -catA3_1 phenicol -cat_1 phenicol -cat_5 phenicol -cat86_1 phenicol -cat_2 phenicol -cat_3 phenicol -cat(pC221)_1 phenicol -cat(pC233)_1 phenicol -cat(pC194)_1 phenicol -catS_1 phenicol -catP_1 phenicol -cmlA1_1 phenicol -cmlA1_2 phenicol -cml_1 phenicol -cmlV_1 phenicol -floR_1 phenicol -floR_2 phenicol -fexA_1 phenicol -fexA_2 phenicol -pexA_1 phenicol -catA1_1 phenicol -catA2_1 phenicol -cat_4 phenicol -catQ_1 phenicol -cmrA_1 phenicol -cmx_1 phenicol -cfr_1 phenicol -cfr_2 phenicol -cfr(B)_3 phenicol -cfr(B)_1 phenicol -cfr(B)_2 phenicol -cfr(C)_1 phenicol -cfr(C)_2 phenicol -cmlB1_1 phenicol -fexB_1 phenicol -EstDL136_1 phenicol -qnrA1_1 quinolone -qnrA2_1 quinolone -qnrA3_1 quinolone -qnrA4_1 quinolone -qnrA5_1 quinolone -qnrA6_1 quinolone -qnrA7_1 quinolone -qnrA8_1 quinolone -qnrB1_1 quinolone -qnrB2_1 quinolone -qnrB3_1 quinolone -qnrB4_1 quinolone -qnrB5_1 quinolone -qnrB6_1 quinolone -qnrB6_2 quinolone -qnrB7_1 quinolone -qnrB8_1 quinolone -qnrB9_1 quinolone -qnrB10_1 quinolone -qnrB10_2 quinolone -qnrB11_1 quinolone -qnrB12_2 quinolone -qnrB13_1 quinolone -qnrB14_1 quinolone -qnrB15_1 quinolone -qnrB16_1 quinolone -qnrB17_1 quinolone -qnrB17_2 quinolone -qnrB18_1 quinolone -qnrB19_1 quinolone -qnrB20_1 quinolone -qnrB21_1 quinolone -qnrB22_1 quinolone -qnrB23_1 quinolone -qnrB24_1 quinolone -qnrB25_1 quinolone -qnrB26_1 quinolone -qnrB27_1 quinolone -qnrB28_1 quinolone -qnrB29_1 quinolone -qnrB30_1 quinolone -qnrB31_1 quinolone -qnrB32_1 quinolone -qnrB33_1 quinolone -qnrB34_1 quinolone -qnrB35_1 quinolone -qnrB36_1 quinolone -qnrB37_1 quinolone -qnrB38_1 quinolone -qnrB39_1 quinolone -qnrB40_1 quinolone -qnrB41_1 quinolone -qnrB42_1 quinolone -qnrB43_1 quinolone -qnrB44_1 quinolone -qnrB45_1 quinolone -qnrB46_1 quinolone -qnrB47_1 quinolone -qnrB48_1 quinolone -qnrB49_1 quinolone -qnrB50_1 quinolone -qnrB51_1 quinolone -qnrB52_1 quinolone -qnrB53_1 quinolone -qnrB54_1 quinolone -qnrB55_1 quinolone -qnrB56_1 quinolone -qnrB57_1 quinolone -qnrB58_1 quinolone -qnrB59_1 quinolone -qnrB60_1 quinolone -qnrB61_1 quinolone -qnrB62_1 quinolone -qnrB64_1 quinolone -qnrB65_1 quinolone -qnrB66_1 quinolone -qnrB67_1 quinolone -qnrB68_1 quinolone -qnrB69_1 quinolone -qnrB70_1 quinolone -qnrB71_1 quinolone -qnrB72_1 quinolone -qnrB73_1 quinolone -qnrB74_1 quinolone -qnrB75_1 quinolone -qnrB76_1 quinolone -qnrB77_1 quinolone -qnrB78_1 quinolone -qnrB80_1 quinolone -qnrB81_1 quinolone -qnrB82_1 quinolone -qnrVC1_1 quinolone -qnrVC3_1 quinolone -qnrVC4_1 quinolone -qnrVC5_1 quinolone -qnrVC6_1 quinolone -qnrVC7_1 quinolone -qnrC_1 quinolone -qnrD1_1 quinolone -qnrD2_1 quinolone -qnrD3_1 quinolone -qnrS1_1 quinolone -qnrS2_1 quinolone -qnrS3_1 quinolone -qnrS4_1 quinolone -qnrS5_1 quinolone -qnrS6_1 quinolone -qnrS7_1 quinolone -qnrS8_1 quinolone -qnrS9_1 quinolone -qnrS10_1 quinolone -qnrS11_1 quinolone -qnrS12_1 quinolone -qnrS13_1 quinolone -qepA_1 quinolone -qepA1_1 quinolone -qepA2_1 quinolone -qepA3_1 quinolone -qepA4_1 quinolone -aac(6')-Ib-cr_1 quinolone -aac(6')-Ib-cr_2 quinolone -oqxA_1 quinolone -oqxB_1 quinolone -qnrE1_1 quinolone -crpP_1 quinolone -ARR-2_1 rifampicin -ARR-3_1 rifampicin -ARR-3_4 rifampicin -ARR-4_1 rifampicin -ARR-5_1 rifampicin -ARR-6_1 rifampicin -ARR-6_2 rifampicin -ARR-6_3 rifampicin -ARR-7_1 rifampicin -sul1_2 sulphonamide -sul1_3 sulphonamide -sul1_5 sulphonamide -sul1_7 sulphonamide -sul1_8 sulphonamide -sul1_9 sulphonamide -sul1_10 sulphonamide -sul1_11 sulphonamide -sul1_14 sulphonamide -sul1_15 sulphonamide -sul1_17 sulphonamide -sul1_18 sulphonamide -sul1_19 sulphonamide -sul1_20 sulphonamide -sul1_21 sulphonamide -sul1_22 sulphonamide -sul1_23 sulphonamide -sul1_24 sulphonamide -sul1_25 sulphonamide -sul1_26 sulphonamide -sul1_27 sulphonamide -sul1_28 sulphonamide -sul1_29 sulphonamide -sul1_30 sulphonamide -sul1_31 sulphonamide -sul1_32 sulphonamide -sul1_33 sulphonamide -sul2_1 sulphonamide -sul2_2 sulphonamide -sul2_3 sulphonamide -sul2_5 sulphonamide -sul2_6 sulphonamide -sul2_7 sulphonamide -sul2_8 sulphonamide -sul2_9 sulphonamide -sul2_10 sulphonamide -sul2_11 sulphonamide -sul2_12 sulphonamide -sul2_13 sulphonamide -sul2_14 sulphonamide -sul2_15 sulphonamide -sul2_17 sulphonamide -sul2_18 sulphonamide -sul2_19 sulphonamide -sul2_20 sulphonamide -sul2_21 sulphonamide -sul3_2 sulphonamide -sul1_34 sulphonamide -sul1_35 sulphonamide -sul1_38 sulphonamide -sul1_39 sulphonamide -sul1_36 sulphonamide -sul1_37 sulphonamide -sul4_1 sulphonamide -tet_1 tetracycline -tet(47)_1 tetracycline -tet(48)_1 tetracycline -tet(49)_1 tetracycline -tet(50)_1 tetracycline -tet(51)_1 tetracycline -tet(52)_1 tetracycline -tet(53)_1 tetracycline -tet(54)_1 tetracycline -tet(55)_1 tetracycline -tet(O/32/O)_4 tetracycline -otr(B)_1 tetracycline -tet(39)_1 tetracycline -tet(33)_1 tetracycline -tet(33)_2 tetracycline -tet(32)_1 tetracycline -tet(32)_2 tetracycline -tet(31)_1 tetracycline -tet(31)_2 tetracycline -tet(44)_1 tetracycline -tet(44)_2 tetracycline -tet(40)_1 tetracycline -tet(40)_2 tetracycline -tet(37)_1 tetracycline -tet(34)_1 tetracycline -otr(A)_1 tetracycline -tet(36)_1 tetracycline -tet(T)_1 tetracycline -tet(T)_2 tetracycline -tet(41)_1 tetracycline -tet(42)_1 tetracycline -tet(43)_1 tetracycline -tet(45)_1 tetracycline -tetA(46)_1 tetracycline -tetB(46)_1 tetracycline -tet(57)_1 tetracycline -tet(59)_1 tetracycline -tetA(60)_1 tetracycline -tetB(60)_1 tetracycline -otr(C)_1 tetracycline -tcr3_1 tetracycline -tet(30)_1 tetracycline -tet(35)_1 tetracycline -tet(A)_1 tetracycline -tet(A)_2 tetracycline -tet(A)_3 tetracycline -tet(A)_4 tetracycline -tet(A)_5 tetracycline -tet(A)_6 tetracycline -tet(G)_1 tetracycline -tet(G)_2 tetracycline -tet(G)_3 tetracycline -tet(E)_1 tetracycline -tet(E)_2 tetracycline -tet(E)_3 tetracycline -tet(D)_1 tetracycline -tet(D)_2 tetracycline -tet(C)_1 tetracycline -tet(C)_2 tetracycline -tet(C)_3 tetracycline -tet(B)_1 tetracycline -tet(B)_2 tetracycline -tet(B)_3 tetracycline -tet(H)_1 tetracycline -tet(H)_2 tetracycline -tet(H)_3 tetracycline -tet(H)_4 tetracycline -tet(O)_1 tetracycline -tet(O)_2 tetracycline -tet(O)_3 tetracycline -tet(M)_1 tetracycline -tet(M)_2 tetracycline -tet(M)_3 tetracycline -tet(M)_4 tetracycline -tet(M)_5 tetracycline -tet(M)_6 tetracycline -tet(M)_7 tetracycline -tet(M)_8 tetracycline -tet(M)_9 tetracycline -tet(M)_10 tetracycline -tet(M)_11 tetracycline -tet(M)_12 tetracycline -tet(M)_13 tetracycline -tet(L)_1 tetracycline -tet(L)_2 tetracycline -tet(L)_3 tetracycline -tet(L)_4 tetracycline -tet(L)_5 tetracycline -tet(L)_6 tetracycline -tet(L)_7 tetracycline -tet(L)_8 tetracycline -tet(K)_1 tetracycline -tet(K)_2 tetracycline -tet(J)_1 tetracycline -tet(J)_2 tetracycline -tet(S)_1 tetracycline -tet(S)_2 tetracycline -tet(S)_3 tetracycline -tet(S/M)_2 tetracycline -tet(Q)_1 tetracycline -tet(Q)_2 tetracycline -tet(Q)_3 tetracycline -tet(Q)_4 tetracycline -tetA(P)_1 tetracycline -tetA(P)_2 tetracycline -tetA(P)_3 tetracycline -tet(Z)_1 tetracycline -tet(Y)_1 tetracycline -tet(Y)_2 tetracycline -tet(X)_1 tetracycline -tet(X)_2 tetracycline -tet(X)_3 tetracycline -tet(W)_1 tetracycline -tet(W)_2 tetracycline -tet(W)_3 tetracycline -tet(W)_4 tetracycline -tet(W)_5 tetracycline -tet(V)_1 tetracycline -tetB(P)_1 tetracycline -tet(O/W)_1 tetracycline -tet(O/W)_2 tetracycline -tet(O/W)_3 tetracycline -tet(O/W)_4 tetracycline -tet(O/W)_5 tetracycline -tet(O/W)-2_1 tetracycline -tet(O/W)-1_1 tetracycline -tet(O/W/O)-3_1 tetracycline -tet(O/W/O)-2_1 tetracycline -tet(O/W/O)-1_1 tetracycline -tet(O/W/32/O)_1 tetracycline -tet(O/W/32/O)_2 tetracycline -tet(O/W/32/O)_5 tetracycline -tet(O/W/32/O/W/O)_1 tetracycline -tet(O/W/32/O/W/O)_2 tetracycline -tet(O/32/O)_1 tetracycline -tet(O/32/O)_2 tetracycline -tet(O/32/O)_3 tetracycline -tet(O/32/O)_5 tetracycline -tet(S/M)_1 tetracycline -tet(W/32/O)_1 tetracycline -tet(W/32/O)_2 tetracycline -tet(W/32/O)_3 tetracycline -tet(W/32/O)_4 tetracycline -tet(X3)_1 tetracycline -tet(X4)_1 tetracycline -tet(X5)_1 tetracycline -dfrA19_1 trimethoprim -dfrA27_1 trimethoprim -dfrA31_1 trimethoprim -dfrA30_1 trimethoprim -dfrK_1 trimethoprim -dfrA23_1 trimethoprim -dfrA17_1 trimethoprim -dfrB2_1 trimethoprim -dfrA14_5 trimethoprim -dfrA25_1 trimethoprim -dfrA10_1 trimethoprim -dfrK_2 trimethoprim -dfrB1_1 trimethoprim -dfrK_3 trimethoprim -dfrB4_1 trimethoprim -dfrB3_2 trimethoprim -dfrA28_2 trimethoprim -dfrA21_1 trimethoprim -dfrA26_1 trimethoprim -dfrA15_4 trimethoprim -dfrA13_1 trimethoprim -dfrG_1 trimethoprim -dfrA6_1 trimethoprim -dfrA20_1 trimethoprim -dfrA3_1 trimethoprim -dfrA5_1 trimethoprim -dfrA8_1 trimethoprim -dfrA9_1 trimethoprim -dfrA14_2 trimethoprim -dfrA16_1 trimethoprim -dfrA18_1 trimethoprim -dfrA24_1 trimethoprim -dfrA32_1 trimethoprim -dfrA33_1 trimethoprim -dfrB3_1 trimethoprim -dfrB5_1 trimethoprim -dfrB6_1 trimethoprim -dfrB7_1 trimethoprim -dfrB8_1 trimethoprim -dfrA1_1 trimethoprim -dfrA1_2 trimethoprim -dfrA1_3 trimethoprim -dfrA1_4 trimethoprim -dfrA1_5 trimethoprim -dfrA1_6 trimethoprim -dfrA1_7 trimethoprim -dfrA1_8 trimethoprim -dfrA1_9 trimethoprim -dfrA1_10 trimethoprim -dfrA1_11 trimethoprim -dfrA1_12 trimethoprim -dfrA1_13 trimethoprim -dfrA1_14 trimethoprim -dfrA1_15 trimethoprim -dfrA1_16 trimethoprim -dfrA1_17 trimethoprim -dfrA12_1 trimethoprim -dfrA12_2 trimethoprim -dfrA12_3 trimethoprim -dfrA12_4 trimethoprim -dfrA12_5 trimethoprim -dfrA12_6 trimethoprim -dfrA12_7 trimethoprim -dfrA12_8 trimethoprim -dfrA12_9 trimethoprim -dfrA12_10 trimethoprim -dfrA14_1 trimethoprim -dfrA14_3 trimethoprim -dfrA14_4 trimethoprim -dfrA15_1 trimethoprim -dfrA15_2 trimethoprim -dfrA15_3 trimethoprim -dfrA16_2 trimethoprim -dfrA16_3 trimethoprim -dfrA16_4 trimethoprim -dfrA22_1 trimethoprim -dfrA22_2 trimethoprim -dfrA22_3 trimethoprim -dfrA22_4 trimethoprim -dfrA22_5 trimethoprim -dfrA29_1 trimethoprim -dfrA5_3 trimethoprim -dfrA5_2 trimethoprim -dfrA5_4 trimethoprim -dfrA6_2 trimethoprim -dfrA7_1 trimethoprim -dfrA7_2 trimethoprim -dfrA7_3 trimethoprim -dfrA7_4 trimethoprim -dfrA7_5 trimethoprim -dfrB1_2 trimethoprim -dfrB2_2 trimethoprim -dfrB4_2 trimethoprim -dfrB4_3 trimethoprim -dfrD_1 trimethoprim -dfrA17_11 trimethoprim -dfrA17_2 trimethoprim -dfrA17_3 trimethoprim -dfrA17_4 trimethoprim -dfrA17_5 trimethoprim -dfrA17_6 trimethoprim -dfrA17_7 trimethoprim -dfrA17_8 trimethoprim -dfrA17_9 trimethoprim -dfrA17_10 trimethoprim -dfrA34_1 trimethoprim
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Tue Mar 21 14:06:11 2023 +0000 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +#