changeset 9:70073df30a06 draft

Uploaded
author greg
date Tue, 21 Mar 2023 14:06:11 +0000 (21 months ago)
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(-) [+]
line wrap: on
line diff
--- 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&lt;designation&gt;.+)\.(?P&lt;ext&gt;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	aminoglycoside
-str_2	aminoglycoside
-str_3	aminoglycoside
-aac(3)-IIIb_2	aminoglycoside
-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
-blaOXA-368_1	beta-lactam
-blaOXA-336_1	beta-lactam
-blaOXA-337_1	beta-lactam
-blaOXA-338_1	beta-lactam
-blaOXA-339_1	beta-lactam
-blaOXA-340_1	beta-lactam
-blaOXA-341_1	beta-lactam
-blaOXA-342_1	beta-lactam
-blaOXA-343_1	beta-lactam
-blaOXA-344_1	beta-lactam
-blaOXA-345_1	beta-lactam
-blaOXA-346_1	beta-lactam
-blaOXA-347_1	beta-lactam
-blaOXA-361_1	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
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-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
--- /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.
+#