Mercurial > repos > greg > draw_amr_matrix
changeset 0:6044ca44e9f6 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 07 Feb 2023 22:13:57 +0000 |
| parents | |
| children | 5c923c77cf5f |
| files | .shed.yml draw_amr_matrix.py draw_amr_matrix.xml macros.xml test-data/amr_gene_drug.tsv test-data/amr_pima_md.bed |
| diffstat | 6 files changed, 3322 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Tue Feb 07 22:13:57 2023 +0000 @@ -0,0 +1,9 @@ +name: draw_amr_matrix +owner: greg +description: Accepts a tabular AMR gene drugs file and a collection of best feature hits and draws an AMR matrix. +long_description: Accepts a tabular AMR gene drugs file and a collection of best feature hits and draws an AMR matrix. +categories: +- Visualization +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/pima/draw_amr_matrix +homepage_url: https://github.com/gregvonkuster/galaxy_tools +type: unrestricted
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/draw_amr_matrix.py Tue Feb 07 22:13:57 2023 +0000 @@ -0,0 +1,117 @@ +#!/usr/bin/env python + +import argparse +import csv +import os + +import numpy +import pandas +import matplotlib.pyplot as pyplot + + +def get_amr_in_feature_hits(feature_hits): + for k in feature_hits.keys(): + if k.lower().find('amr') >= 0: + return feature_hits[k] + return None + + +def draw_amr_matrix(feature_hits_files, amr_gene_drug_file, output_dir): + ofh = open('process_log', 'w') + + # Read feature_hits_files. + feature_hits = pandas.Series(dtype=object) + for feature_hits_file in feature_hits_files: + feature_name = os.path.basename(feature_hits_file) + # Make sure the file is not empty. + if os.path.isfile(feature_hits_file) and os.path.getsize(feature_hits_file) > 0: + best_hits = pandas.read_csv(filepath_or_buffer=feature_hits_file, sep='\t', header=None) + ofh.write("\nFeature file %s will be processed\n" % os.path.basename(feature_hits_file)) + else: + ofh.write("\nEmpty feature file %s will NOT be processed\n" % os.path.basename(feature_hits_file)) + best_hits = None + feature_hits[feature_name] = best_hits + + amr_hits = get_amr_in_feature_hits(feature_hits) + ofh.write("\namr_hits:\n%s\n" % str(amr_hits)) + if amr_hits is not None: + amr_to_draw = pandas.DataFrame(columns=['gene', 'drug']) + ofh.write("\namr_to_draw:\n%s\n" % str(amr_to_draw)) + # Read amr_drug_gene_file. + amr_gene_drug = pandas.read_csv(amr_gene_drug_file, index_col=None, sep='\t', quoting=csv.QUOTE_NONE, header=None) + ofh.write("\namr_gene_drug:\n%s\n" % str(amr_gene_drug)) + + # Roll up AMR gene hits. + ofh.write("\namr_hits.shape[0]:%s\n" % str(amr_hits.shape[0])) + if amr_hits.shape[0] > 0: + for gene_idx, gene in amr_hits.iterrows(): + ofh.write("gene_idx:%s\n" % str(gene_idx)) + ofh.write("gene:%s\n" % str(gene)) + gene_name = gene[3] + ofh.write("gene_name: %s\n" % str(gene_name)) + ofh.write("amr_gene_drug[0]: %s\n" % str(amr_gene_drug[0])) + drugs = amr_gene_drug.loc[amr_gene_drug[0] == gene_name, :][1] + ofh.write("drugs:%s\n" % str(drugs)) + for drug in drugs: + 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)) + + amr_mutations = pandas.Series(dtype=object) + if amr_mutations.shape[0] > 0: + # Roll up potentially resistance conferring mutations. + # TODO: may need to populate this if we need to use call_amr_mutations. + for mutation_region, mutation_hits in amr_mutations.iteritems(): + for mutation_idx, mutation_hit in mutation_hits.iterrows(): + mutation_name = mutation_region + ' ' + mutation_hit['REF'] + '->' + mutation_hit['ALT'] + amr_to_draw = amr_to_draw.append(pandas.Series([mutation_name, mutation_hit['DRUG']], name=amr_to_draw.shape[0], index=amr_to_draw.columns)) + + amr_deletions = pandas.DataFrame() + if amr_deletions.shape[0] > 0: + # Roll up deletions that might confer resistance. + # TODO: may need to populate this if we need to use call_insertions. + 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)) + + 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(): + amr_matrix.loc[hit[0], hit[1]] = 1 + amr_matrix_png = os.path.join(output_dir, 'amr_matrix.png') + int_matrix = amr_matrix[amr_matrix.columns].astype(int) + figure, axis = pyplot.subplots() + axis.invert_yaxis() + axis.set_yticks(numpy.arange(0.5, len(amr_matrix.index)), minor=False) + axis.set_yticklabels(int_matrix.index.values) + axis.set_xticks(numpy.arange(0.5, len(amr_matrix.columns)), minor=False) + axis.set_xticklabels(amr_matrix.columns.values, rotation=90) + axis.xaxis.tick_top() + axis.xaxis.set_label_position('top') + pyplot.tight_layout() + pyplot.savefig(amr_matrix_png, dpi=300) + else: + ofh.write("\nEmpty AMR matrix, nothing to draw...\n") + ofh.close() + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + + parser.add_argument('--amr_gene_drug_file', action='store', dest='amr_gene_drug_file', help='AMR_gene_drugs tsv file') + parser.add_argument('--feature_hits_dir', action='store', dest='feature_hits_dir', help='Directory of tabular files containing feature hits') + parser.add_argument('--output_dir', action='store', dest='output_dir', help='Output directory') + + args = parser.parse_args() + + # Get thge collection of feature hits files. The collection + # will be sorted alphabetically and will contain 2 files + # named something like AMR_CDS_311_2022_12_20.fasta and + # Incompatibility_Groups_2023_01_01.fasta. + feature_hits_files = [] + for file_name in sorted(os.listdir(args.feature_hits_dir)): + file_path = os.path.abspath(os.path.join(args.feature_hits_dir, file_name)) + feature_hits_files.append(file_path) + + draw_amr_matrix(feature_hits_files, args.amr_gene_drug_file, args.output_dir)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/draw_amr_matrix.xml Tue Feb 07 22:13:57 2023 +0000 @@ -0,0 +1,67 @@ +<tool id="draw_amr_matrix" name="PIMA: draw AMR matrix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>of genes and drugs</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +#import re + +mkdir feature_hits_dir && +mkdir output_dir && + +#for $i in $feature_hits: + #set file_name = $i.file_name + #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) + ln -s '$file_name' 'feature_hits_dir/$identifier' && +#end for + +python '$__tool_directory__/draw_amr_matrix.py' +--amr_gene_drug '$amr_gene_drug' +--feature_hits_dir 'feature_hits_dir' +--output_dir 'output_dir' +#if str($output_process_log) == 'yes': + && mv 'process_log' '$process_log' +#end if +]]></command> + <inputs> + <param argument="--amr_gene_drug" type="data" format="tabular,tsv" label="Tabular AMR gene drugs file"/> + <param argument="--feature_hits" format="bed" type="data_collection" collection_type="list" label="Collection of feature hits BED files"/> + <param name="output_process_log" type="select" display="radio" label="Output process log file?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + </inputs> + <outputs> + <data name="process_log" format="txt" label="${tool.name} on ${on_string} (Process log)"> + <filter>output_process_log == 'yes'</filter> + </data> + <collection name="amr_matrix_png" type="list" format="png"> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>png)" directory="output_dir"/> + </collection> + </outputs> + <tests> + <test> + <param name="amr_gene_drug" value="amr_gene_drug.tsv" ftype="tsv"/> + <param name="feature_hits"> + <collection type="list"> + <element name="amr_pima_md" value="amr_pima_md.bed"/> + </collection> + </param> + <output_collection name="amr_matrix_png" type="list" count="1"> + <element name="amr_matrix" ftype="png"> + <assert_contents> + <has_size value="38309" delta="500"/> + </assert_contents> + </element> + </output_collection> + </test> + </tests> + <help> +**What it does** + +Accepts a tabular AMR gene drugs file and a collection of best feature hits and draws an AMR matrix. + </help> + <expand macro="citations"/> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Feb 07 22:13:57 2023 +0000 @@ -0,0 +1,22 @@ +<macros> + <token name="@TOOL_VERSION@">1.0.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.01</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="9.1">coreutils</requirement> + <requirement type="package" version="5.1.0">gawk</requirement> + <requirement type="package" version="3.4">grep</requirement> + <requirement type="package" version="3.6.2">matplotlib</requirement> + <requirement type="package" version="1.23.5">numpy</requirement> + <requirement type="package" version="1.5.2">pandas</requirement> + <requirement type="package" version="1.16.1">samtools</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/011650</citation> + </citations> + </xml> +</macros> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amr_gene_drug.tsv Tue Feb 07 22:13:57 2023 +0000 @@ -0,0 +1,3105 @@ +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 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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 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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 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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