update AMRFinderPlus test db

oschwengers · Mar 7, 2024 · 9e8a24d · 9e8a24d
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diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3f b/test/db-light/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3f
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3i b/test/db-light/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3i
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3m b/test/db-light/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3m
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3p b/test/db-light/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3p
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab b/test/db-light/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMRProt-suppress b/test/db-light/amrfinderplus-db/2021-09-30.1/AMRProt-suppress
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab b/test/db-light/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMRProt.phr b/test/db-light/amrfinderplus-db/2021-09-30.1/AMRProt.phr
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMRProt.pin b/test/db-light/amrfinderplus-db/2021-09-30.1/AMRProt.pin
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMRProt.psq b/test/db-light/amrfinderplus-db/2021-09-30.1/AMRProt.psq
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMRProt.ptf b/test/db-light/amrfinderplus-db/2021-09-30.1/AMRProt.ptf
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMRProt.pto b/test/db-light/amrfinderplus-db/2021-09-30.1/AMRProt.pto
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMR_CDS.nhr b/test/db-light/amrfinderplus-db/2021-09-30.1/AMR_CDS.nhr
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMR_CDS.nin b/test/db-light/amrfinderplus-db/2021-09-30.1/AMR_CDS.nin
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMR_CDS.not b/test/db-light/amrfinderplus-db/2021-09-30.1/AMR_CDS.not
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMR_CDS.nsq b/test/db-light/amrfinderplus-db/2021-09-30.1/AMR_CDS.nsq
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMR_CDS.ntf b/test/db-light/amrfinderplus-db/2021-09-30.1/AMR_CDS.ntf
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/AMR_CDS.nto b/test/db-light/amrfinderplus-db/2021-09-30.1/AMR_CDS.nto
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/database_format_version.txt b/test/db-light/amrfinderplus-db/2021-09-30.1/database_format_version.txt
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/taxgroup.tab b/test/db-light/amrfinderplus-db/2021-09-30.1/taxgroup.tab
diff --git a/test/db-light/amrfinderplus-db/2021-09-30.1/version.txt b/test/db-light/amrfinderplus-db/2021-09-30.1/version.txt
diff --git a/test/db-light/amrfinderplus-db/latest b/test/db-light/amrfinderplus-db/latest
@@ -1 +1 @@
-2021-09-30.1
+../../db/amrfinderplus-db/2024-01-31.1
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3f b/test/db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3f
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3i b/test/db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3i
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3m b/test/db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3m
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3p b/test/db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3p
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab b/test/db/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMRProt-suppress b/test/db/amrfinderplus-db/2021-09-30.1/AMRProt-suppress
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab b/test/db/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMRProt.pdb b/test/db/amrfinderplus-db/2021-09-30.1/AMRProt.pdb
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMRProt.phr b/test/db/amrfinderplus-db/2021-09-30.1/AMRProt.phr
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMRProt.pin b/test/db/amrfinderplus-db/2021-09-30.1/AMRProt.pin
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMRProt.psq b/test/db/amrfinderplus-db/2021-09-30.1/AMRProt.psq
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMRProt.pto b/test/db/amrfinderplus-db/2021-09-30.1/AMRProt.pto
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMR_CDS.ndb b/test/db/amrfinderplus-db/2021-09-30.1/AMR_CDS.ndb
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nhr b/test/db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nhr
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nin b/test/db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nin
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMR_CDS.not b/test/db/amrfinderplus-db/2021-09-30.1/AMR_CDS.not
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nsq b/test/db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nsq
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nto b/test/db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nto
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/database_format_version.txt b/test/db/amrfinderplus-db/2021-09-30.1/database_format_version.txt
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/fam.tab b/test/db/amrfinderplus-db/2021-09-30.1/fam.tab
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/taxgroup.tab b/test/db/amrfinderplus-db/2021-09-30.1/taxgroup.tab
diff --git a/test/db/amrfinderplus-db/2021-09-30.1/version.txt b/test/db/amrfinderplus-db/2021-09-30.1/version.txt
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMR.LIB.h3f b/test/db/amrfinderplus-db/2024-01-31.1/AMR.LIB.h3f
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMR.LIB.h3i b/test/db/amrfinderplus-db/2024-01-31.1/AMR.LIB.h3i
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMR.LIB.h3m b/test/db/amrfinderplus-db/2024-01-31.1/AMR.LIB.h3m
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMR.LIB.h3p b/test/db/amrfinderplus-db/2024-01-31.1/AMR.LIB.h3p
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMRProt-mutation.tab b/test/db/amrfinderplus-db/2024-01-31.1/AMRProt-mutation.tab
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMRProt-suppress b/test/db/amrfinderplus-db/2024-01-31.1/AMRProt-suppress
@@ -0,0 +1,17 @@
+#taxgroup	protein_accession	protein_gi
+Escherichia	AAA21095.1	151858
+Escherichia	AAA21096.1	151859
+Escherichia	AAB09628.1	1061418
+Escherichia	BAA24823.1	2879920
+Escherichia	BAA24824.1	2879921
+Escherichia	BAA15331.2	85675040
+Escherichia	BAE77395.1	85676145
+Escherichia	BAE77620.1	85676370
+Escherichia	BAE77793.1	85676543
+Klebsiella_oxytoca	BAA24824.1	2879921
+Klebsiella_oxytoca	BAB89353.1	20152201
+Klebsiella_pneumoniae	ABR76310.1	150954280
+Salmonella	BAE77395.1	85676145
+Staphylococcus_pseudintermedius	AAA25637.1	150728
+Staphylococcus_pseudintermedius	AAA27588.1	155345
+Vibrio_cholerae	ABQ18953.1	146314413
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMRProt-susceptible.tab b/test/db/amrfinderplus-db/2024-01-31.1/AMRProt-susceptible.tab
@@ -0,0 +1,27 @@
+#taxgroup	gene_symbol	accession_version	resistance_cutoff	class	subclass	resistance_protein_name
+Neisseria_gonorrhoeae	pbp2	WP_003703066.1	           94.000000	BETA-LACTAM	BETA-LACTAM	Neisseria_gonorrhoeae_beta-lactam_resistant_PBP2
+Streptococcus_pneumoniae	pbp1a	WP_001039998.1	           99.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A
+Streptococcus_pneumoniae	pbp1a	WP_001040004.1	           99.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A
+Streptococcus_pneumoniae	pbp1a	WP_001040010.1	           99.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A
+Streptococcus_pneumoniae	pbp1a	WP_001040013.1	           99.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A
+Streptococcus_pneumoniae	pbp1a	WP_050078510.1	           99.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A
+Streptococcus_pneumoniae	pbp1a	WP_050208712.1	           99.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A
+Streptococcus_pneumoniae	pbp1a	WP_054370471.1	           99.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A
+Streptococcus_pneumoniae	pbp2b	WP_001224867.1	           99.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B
+Streptococcus_pneumoniae	pbp2b	WP_001224871.1	           99.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B
+Streptococcus_pneumoniae	pbp2b	WP_001224884.1	           99.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B
+Streptococcus_pneumoniae	pbp2b	WP_001224885.1	           99.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B
+Streptococcus_pneumoniae	pbp2b	WP_001224886.1	           99.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B
+Streptococcus_pneumoniae	pbp2b	WP_061634854.1	           99.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B
+Streptococcus_pneumoniae	pbp2x	WP_000872264.1	           98.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X
+Streptococcus_pneumoniae	pbp2x	WP_000872267.1	           98.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X
+Streptococcus_pneumoniae	pbp2x	WP_000872270.1	           98.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X
+Streptococcus_pneumoniae	pbp2x	WP_000872271.1	           98.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X
+Streptococcus_pneumoniae	pbp2x	WP_000872273.1	           98.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X
+Streptococcus_pneumoniae	pbp2x	WP_000872275.1	           98.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X
+Streptococcus_pneumoniae	pbp2x	WP_000872277.1	           98.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X
+Streptococcus_pneumoniae	pbp2x	WP_000872282.1	           98.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X
+Streptococcus_pneumoniae	pbp2x	WP_033707918.1	           98.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X
+Streptococcus_pneumoniae	pbp2x	WP_050293540.1	           98.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X
+Streptococcus_pneumoniae	pbp2x	WP_054364452.1	           98.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X
+Streptococcus_pneumoniae	pbp2x	WP_061745305.1	           98.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X
diff --git a/...amrfinderplus-db/2021-09-30.1/AMRProt.pdb → ...amrfinderplus-db/2024-01-31.1/AMRProt.pdb b/...amrfinderplus-db/2021-09-30.1/AMRProt.pdb → ...amrfinderplus-db/2024-01-31.1/AMRProt.pdb
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMRProt.phr b/test/db/amrfinderplus-db/2024-01-31.1/AMRProt.phr
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMRProt.pin b/test/db/amrfinderplus-db/2024-01-31.1/AMRProt.pin
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMRProt.pjs b/test/db/amrfinderplus-db/2024-01-31.1/AMRProt.pjs
@@ -0,0 +1,22 @@
+{
+  "version": "1.2",
+  "dbname": "AMRProt",
+  "dbtype": "Protein",
+  "db-version": 5,
+  "description": "/tmp/amrfinder_index.rIIqgh/db/AMRProt",
+  "number-of-letters": 2858944,
+  "number-of-sequences": 8280,
+  "last-updated": "2024-03-07T11:33:00",
+  "number-of-volumes": 1,
+  "bytes-total": 4700030,
+  "bytes-to-cache": 2933585,
+  "files": [
+    "AMRProt.pdb",
+    "AMRProt.phr",
+    "AMRProt.pin",
+    "AMRProt.pot",
+    "AMRProt.psq",
+    "AMRProt.ptf",
+    "AMRProt.pto"
+  ]
+}
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMRProt.psq b/test/db/amrfinderplus-db/2024-01-31.1/AMRProt.psq
diff --git a/...amrfinderplus-db/2021-09-30.1/AMRProt.ptf → ...amrfinderplus-db/2024-01-31.1/AMRProt.ptf b/...amrfinderplus-db/2021-09-30.1/AMRProt.ptf → ...amrfinderplus-db/2024-01-31.1/AMRProt.ptf
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMRProt.pto b/test/db/amrfinderplus-db/2024-01-31.1/AMRProt.pto
diff --git a/...amrfinderplus-db/2021-09-30.1/AMR_CDS.ndb → ...amrfinderplus-db/2024-01-31.1/AMR_CDS.ndb b/...amrfinderplus-db/2021-09-30.1/AMR_CDS.ndb → ...amrfinderplus-db/2024-01-31.1/AMR_CDS.ndb
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMR_CDS.nhr b/test/db/amrfinderplus-db/2024-01-31.1/AMR_CDS.nhr
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMR_CDS.nin b/test/db/amrfinderplus-db/2024-01-31.1/AMR_CDS.nin
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMR_CDS.njs b/test/db/amrfinderplus-db/2024-01-31.1/AMR_CDS.njs
@@ -0,0 +1,22 @@
+{
+  "version": "1.2",
+  "dbname": "AMR_CDS",
+  "dbtype": "Nucleotide",
+  "db-version": 5,
+  "description": "/tmp/amrfinder_index.rIIqgh/db/AMR_CDS",
+  "number-of-letters": 8187001,
+  "number-of-sequences": 8038,
+  "last-updated": "2024-03-07T11:33:00",
+  "number-of-volumes": 1,
+  "bytes-total": 3834407,
+  "bytes-to-cache": 2149092,
+  "files": [
+    "AMR_CDS.ndb",
+    "AMR_CDS.nhr",
+    "AMR_CDS.nin",
+    "AMR_CDS.not",
+    "AMR_CDS.nsq",
+    "AMR_CDS.ntf",
+    "AMR_CDS.nto"
+  ]
+}
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMR_CDS.not b/test/db/amrfinderplus-db/2024-01-31.1/AMR_CDS.not
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMR_CDS.nsq b/test/db/amrfinderplus-db/2024-01-31.1/AMR_CDS.nsq
diff --git a/...amrfinderplus-db/2021-09-30.1/AMR_CDS.ntf → ...amrfinderplus-db/2024-01-31.1/AMR_CDS.ntf b/...amrfinderplus-db/2021-09-30.1/AMR_CDS.ntf → ...amrfinderplus-db/2024-01-31.1/AMR_CDS.ntf
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/AMR_CDS.nto b/test/db/amrfinderplus-db/2024-01-31.1/AMR_CDS.nto
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/database_format_version.txt b/test/db/amrfinderplus-db/2024-01-31.1/database_format_version.txt
@@ -0,0 +1 @@
+3.12.1
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		2021-09-30.1
		../../db/amrfinderplus-db/2024-01-31.1