# HG changeset patch
# User greg
# Date 1675808037 0
# Node ID 6044ca44e9f6318225febec690fa2be6b15384ee

Uploaded

diff -r 000000000000 -r 6044ca44e9f6 .shed.yml
--- /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
diff -r 000000000000 -r 6044ca44e9f6 draw_amr_matrix.py
--- /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)
diff -r 000000000000 -r 6044ca44e9f6 draw_amr_matrix.xml
--- /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&lt;designation&gt;.+)\.(?P&lt;ext&gt;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>
+
diff -r 000000000000 -r 6044ca44e9f6 macros.xml
--- /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>
+
diff -r 000000000000 -r 6044ca44e9f6 test-data/amr_gene_drug.tsv
--- /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
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+aac(3)-IIa_2	aminoglycoside
+aac(3)-IIa_3	aminoglycoside
+aac(3)-IIa_4	aminoglycoside
+aac(3)-IIa_5	aminoglycoside
+aac(3)-IV_1	aminoglycoside
+aac(3)-VIa_2	aminoglycoside
+aph(3')-Ib_2	aminoglycoside
+ant(9)-Ia_2	aminoglycoside
+aadA24_2	aminoglycoside
+aadA8b_1	aminoglycoside
+aadA2b_1	aminoglycoside
+aac(6')-Ii_1	aminoglycoside
+aac(3)-XI_1	aminoglycoside
+aac(3)-VIII_1	aminoglycoside
+aac(3)-VIII_2	aminoglycoside
+aac(3)-VIII_3	aminoglycoside
+kmr_1	aminoglycoside
+blaNDM-19_1	beta-lactam
+blaNDM-20_1	beta-lactam
+blaNDM-21_1	beta-lactam
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+blaCTX-M-9_1	beta-lactam
+blaCTX-M-10_1	beta-lactam
+blaCTX-M-12_1	beta-lactam
+blaCTX-M-13_2	beta-lactam
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+blaCTX-M-14b_1	beta-lactam
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+blaCTX-M-17_1	beta-lactam
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+blaCTX-M-20_1	beta-lactam
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+blaCTX-M-23_1	beta-lactam
+blaCTX-M-24_1	beta-lactam
+blaCTX-M-25_1	beta-lactam
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+blaCTX-M-83_1	beta-lactam
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+blaCTX-M-85_1	beta-lactam
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+blaCTX-M-90_1	beta-lactam
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+blaCTX-M-100_1	beta-lactam
+blaCTX-M-101_1	beta-lactam
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+blaCTX-M-103_1	beta-lactam
+blaCTX-M-104_1	beta-lactam
+blaCTX-M-105_1	beta-lactam
+blaCTX-M-110_1	beta-lactam
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+blaCTX-M-125_1	beta-lactam
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+blaCTX-M-139_1	beta-lactam
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+blaIMP-68_1	beta-lactam
+blaIMP-6_1	beta-lactam
+blaIMP-9_1	beta-lactam
+blaIMP-10_1	beta-lactam
+blaIMP-13_1	beta-lactam
+blaIMP-25_1	beta-lactam
+blaIMP-71_1	beta-lactam
+blaIMP-73_1	beta-lactam
+blaIMP-74_1	beta-lactam
+blaIMP-75_1	beta-lactam
+blaVIM-57_1	beta-lactam
+blaVIM-56_1	beta-lactam
+blaNDM-22_1	beta-lactam
+blaNDM-23_1	beta-lactam
+blaNDM-24_1	beta-lactam
+blaKPC-13_1	beta-lactam
+blaKPC-12_1	beta-lactam
+blaKPC-22_1	beta-lactam
+blaKPC-21_1	beta-lactam
+blaKPC-19_1	beta-lactam
+blaKPC-18_1	beta-lactam
+blaKPC-17_1	beta-lactam
+blaKPC-30_1	beta-lactam
+blaKPC-29_1	beta-lactam
+blaKPC-28_1	beta-lactam
+blaKPC-27_1	beta-lactam
+blaKPC-26_1	beta-lactam
+blaKPC-25_1	beta-lactam
+blaKPC-24_1	beta-lactam
+blaKPC-23_1	beta-lactam
+blaKPC-31_1	beta-lactam
+blaKPC-32_1	beta-lactam
+blaKPC-33_1	beta-lactam
+blaKPC-34_1	beta-lactam
+blaKPC-35_1	beta-lactam
+blaCTX-M-148_1	beta-lactam
+blaCTX-M-150_1	beta-lactam
+blaCTX-M-151_1	beta-lactam
+blaCTX-M-155_1	beta-lactam
+blaCTX-M-156_1	beta-lactam
+blaCTX-M-157_1	beta-lactam
+blaCTX-M-158_1	beta-lactam
+blaCTX-M-159_1	beta-lactam
+blaCTX-M-160_1	beta-lactam
+blaCTX-M-161_1	beta-lactam
+blaCTX-M-162_1	beta-lactam
+blaCTX-M-163_1	beta-lactam
+blaCTX-M-164_1	beta-lactam
+blaCTX-M-165_1	beta-lactam
+blaCTX-M-166_1	beta-lactam
+blaCTX-M-167_1	beta-lactam
+blaCTX-M-168_1	beta-lactam
+blaCTX-M-169_1	beta-lactam
+blaCTX-M-170_1	beta-lactam
+blaCTX-M-171_1	beta-lactam
+blaCTX-M-172_1	beta-lactam
+blaCTX-M-173_1	beta-lactam
+blaCTX-M-174_1	beta-lactam
+blaCTX-M-175_1	beta-lactam
+blaCTX-M-176_1	beta-lactam
+blaCTX-M-177_1	beta-lactam
+blaCTX-M-179_1	beta-lactam
+blaCTX-M-180_1	beta-lactam
+blaCTX-M-181_1	beta-lactam
+blaCTX-M-182_1	beta-lactam
+blaCTX-M-183_1	beta-lactam
+blaCTX-M-184_1	beta-lactam
+blaCTX-M-186_1	beta-lactam
+blaCTX-M-188_1	beta-lactam
+blaCTX-M-189_1	beta-lactam
+blaCTX-M-190_1	beta-lactam
+blaCTX-M-191_1	beta-lactam
+blaCTX-M-192_1	beta-lactam
+blaCTX-M-193_1	beta-lactam
+blaCTX-M-194_1	beta-lactam
+blaCTX-M-195_1	beta-lactam
+blaCTX-M-196_1	beta-lactam
+blaCTX-M-197_1	beta-lactam
+blaCTX-M-198_1	beta-lactam
+blaCTX-M-199_1	beta-lactam
+blaCTX-M-200_1	beta-lactam
+blaCTX-M-201_1	beta-lactam
+blaCTX-M-202_1	beta-lactam
+blaCTX-M-203_1	beta-lactam
+blaCTX-M-204_1	beta-lactam
+blaCTX-M-206_1	beta-lactam
+blaCTX-M-207_1	beta-lactam
+blaCTX-M-208_1	beta-lactam
+blaCTX-M-209_1	beta-lactam
+blaCTX-M-210_1	beta-lactam
+blaCTX-M-211_1	beta-lactam
+blaCTX-M-212_1	beta-lactam
+blaCTX-M-213_1	beta-lactam
+blaCTX-M-214_1	beta-lactam
+blaCTX-M-216_1	beta-lactam
+blaCTX-M-217_1	beta-lactam
+blaCTX-M-218_1	beta-lactam
+blaCTX-M-219_1	beta-lactam
+blaCTX-M-220_1	beta-lactam
+blaCTX-M-7_1	beta-lactam
+blaCTX-M-73_1	beta-lactam
+blaCTX-M-122_1	beta-lactam
+blaCTX-M-127_1	beta-lactam
+blaCTX-M-137_1	beta-lactam
+blaCTX-M-138_1	beta-lactam
+blaCTX-M-141_1	beta-lactam
+blaCTX-M-144_1	beta-lactam
+blaCTX-M-146_1	beta-lactam
+blaCTX-M-2_1	beta-lactam
+blaCTX-M-5_1	beta-lactam
+blaCTX-M-3_1	beta-lactam
+blaCTX-M-79_1	beta-lactam
+blaCTX-M-59_1	beta-lactam
+blaCTX-M-63_2	beta-lactam
+blaCTX-M-65_1	beta-lactam
+blaCTX-M-55_1	beta-lactam
+blaCTX-M-52_1	beta-lactam
+blaCTX-M-37_1	beta-lactam
+blaCTX-M-38_1	beta-lactam
+blaCTX-M-22_1	beta-lactam
+blaCTX-M-26_1	beta-lactam
+blaCTX-M-27_1	beta-lactam
+blaCTX-M-15_1	beta-lactam
+blaCMY-156_1	beta-lactam
+blaCMY-155_1	beta-lactam
+blaCMY-154_1	beta-lactam
+blaCMY-153_1	beta-lactam
+blaCMY-152_1	beta-lactam
+blaCMY-151_1	beta-lactam
+blaCMY-150_1	beta-lactam
+blaCMY-149_1	beta-lactam
+blaCMY-148_1	beta-lactam
+blaCMY-147_1	beta-lactam
+blaCMY-146_1	beta-lactam
+blaCMY-145_1	beta-lactam
+blaCMY-144_1	beta-lactam
+blaCMY-143_1	beta-lactam
+blaCMY-142_1	beta-lactam
+blaCMY-141_1	beta-lactam
+blaCMY-140_1	beta-lactam
+blaCMY-139_1	beta-lactam
+blaCMY-138_1	beta-lactam
+blaCMY-135_1	beta-lactam
+blaCMY-134_1	beta-lactam
+blaCMY-133_1	beta-lactam
+blaCMY-132_1	beta-lactam
+blaCMY-131_1	beta-lactam
+blaCMY-130_1	beta-lactam
+blaCMY-129_1	beta-lactam
+blaCMY-128_1	beta-lactam
+blaCMY-127_1	beta-lactam
+blaCMY-125_1	beta-lactam
+blaCMY-124_1	beta-lactam
+blaCMY-122_1	beta-lactam
+blaCMY-121_1	beta-lactam
+blaCMY-119_1	beta-lactam
+blaCMY-118_1	beta-lactam
+blaCMY-117_1	beta-lactam
+blaCMY-116_1	beta-lactam
+blaCMY-115_1	beta-lactam
+blaCMY-114_1	beta-lactam
+blaCMY-113_1	beta-lactam
+blaCMY-112_1	beta-lactam
+blaCMY-111_1	beta-lactam
+blaCMY-110_2	beta-lactam
+blaCMY-109_1	beta-lactam
+blaCMY-108_1	beta-lactam
+blaCMY-107_1	beta-lactam
+blaCMY-106_1	beta-lactam
+blaCMY-105_1	beta-lactam
+blaCMY-104_2	beta-lactam
+blaCMY-103_1	beta-lactam
+blaCMY-102_1	beta-lactam
+blaCMY-101_1	beta-lactam
+blaCMY-100_1	beta-lactam
+blaCMY-97_1	beta-lactam
+blaCMY-96_1	beta-lactam
+blaCMY-93_1	beta-lactam
+blaCMY-90_1	beta-lactam
+blaCMY-89_1	beta-lactam
+blaCMY-86_1	beta-lactam
+blaCMY-85_1	beta-lactam
+blaCMY-82_1	beta-lactam
+blaCMY-59_1	beta-lactam
+blaCMY-50_1	beta-lactam
+blaCMY-43_1	beta-lactam
+blaCMY-39_1	beta-lactam
+blaCMY-31_1	beta-lactam
+blaCMY-30_1	beta-lactam
+blaCMY-16_1	beta-lactam
+blaCMY-10_1	beta-lactam
+blaCMY-11_1	beta-lactam
+blaCMY-8b_1	beta-lactam
+blaCMY-4_1	beta-lactam
+blaCMY-2b_1	beta-lactam
+blaDHA-27_1	beta-lactam
+blaDHA-26_1	beta-lactam
+blaDHA-25_1	beta-lactam
+blaDHA-24_1	beta-lactam
+blaDHA-23_1	beta-lactam
+blaDHA-22_1	beta-lactam
+blaDHA-21_1	beta-lactam
+blaDHA-20_1	beta-lactam
+blaDHA-19_1	beta-lactam
+blaDHA-18_1	beta-lactam
+blaDHA-17_1	beta-lactam
+blaDHA-16_1	beta-lactam
+blaDHA-15_1	beta-lactam
+blaDHA-14_1	beta-lactam
+blaDHA-13_1	beta-lactam
+blaDHA-12_1	beta-lactam
+blaDHA-10_1	beta-lactam
+blaDHA-9_1	beta-lactam
+blaDHA-4_1	beta-lactam
+blaACC-7_1	beta-lactam
+blaACC-5_1	beta-lactam
+blaACC-4_2	beta-lactam
+blaACC-4_3	beta-lactam
+blaACC-1_2	beta-lactam
+blaACC-1_1	beta-lactam
+blaACC-1d_1	beta-lactam
+blaACC-1c_1	beta-lactam
+blaACC-1b_1	beta-lactam
+blaACC-1a_1	beta-lactam
+blaTEM-52_1	beta-lactam
+blaTEM-40_1	beta-lactam
+blaTEM-36_1	beta-lactam
+blaTEM-35_1	beta-lactam
+blaTEM-32_1	beta-lactam
+blaTEM-26_1	beta-lactam
+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
diff -r 000000000000 -r 6044ca44e9f6 test-data/amr_pima_md.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amr_pima_md.bed	Tue Feb 07 22:13:57 2023 +0000
@@ -0,0 +1,2 @@
+contig_5	1663151	1664073	mph(K)_1	0.97616	-	contig_5	1663151	1664073	922
+contig_5	3420894	3421748	aadK_1	0.9848	+	contig_5	3420894	3421748	854