Bump AMRFinderplus dependency to v4.0.3 (#343)

* update AMRFinderPlus test db compatible to v4.0.3 * bump amrfinderplus dependency to v4.0.3
oschwengers · Nov 4, 2024 · 518253a · 518253a
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diff --git a/bakta/utils.py b/bakta/utils.py
@@ -47,7 +47,7 @@ def print_version(self):
 DEPENDENCY_DIAMOND = (Version(2, 1, 10), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Diamond', ('diamond', 'help'), ['--skip-cds', '--skip-sorf'])
 DEPENDENCY_DEEPSIG = (Version(1, 2, 5), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'DeepSig', ('deepsig', '--version'), ['--gram ?'])
 DEPENDENCY_BLASTN = (Version(2, 14, 0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Blastn', ('blastn', '-version'), ['--skip-ori'])
-DEPENDENCY_AMRFINDERPLUS = (Version(3, 11, 26), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'AMRFinderPlus', ('amrfinder', '--version'), ['--skip-cds'])
+DEPENDENCY_AMRFINDERPLUS = (Version(4, 0, 3), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'AMRFinderPlus', ('amrfinder', '--version'), ['--skip-cds'])
 DEPENDENCY_CIRCOS = (Version(0, 69, 8), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Circos', ('circos', '--version'), ['--skip-plot'])
 
 

diff --git a/environment.yml b/environment.yml
@@ -17,5 +17,5 @@ dependencies:
   - pyhmmer>=0.10.15
   - diamond>=2.1.10
   - blast>=2.14.0
-  - ncbi-amrfinderplus>=3.11.26
+  - ncbi-amrfinderplus>=4.0.3
   - circos>=0.69.8
diff --git a/test/db-light/amrfinderplus-db b/test/db-light/amrfinderplus-db
@@ -0,0 +1 @@
+../db/amrfinderplus-db
diff --git a/test/db-light/amrfinderplus-db/latest b/test/db-light/amrfinderplus-db/latest
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/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.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
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
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
diff --git a/test/db/amrfinderplus-db/2024-01-31.1/version.txt b/test/db/amrfinderplus-db/2024-01-31.1/version.txt
diff --git a/...amrfinderplus-db/2024-01-31.1/AMR.LIB.h3f → ...amrfinderplus-db/2024-10-22.1/AMR.LIB.h3f b/...amrfinderplus-db/2024-01-31.1/AMR.LIB.h3f → ...amrfinderplus-db/2024-10-22.1/AMR.LIB.h3f
diff --git a/test/db/amrfinderplus-db/2024-10-22.1/AMR.LIB.h3i b/test/db/amrfinderplus-db/2024-10-22.1/AMR.LIB.h3i
diff --git a/...amrfinderplus-db/2024-01-31.1/AMR.LIB.h3m → ...amrfinderplus-db/2024-10-22.1/AMR.LIB.h3m b/...amrfinderplus-db/2024-01-31.1/AMR.LIB.h3m → ...amrfinderplus-db/2024-10-22.1/AMR.LIB.h3m
diff --git a/...amrfinderplus-db/2024-01-31.1/AMR.LIB.h3p → ...amrfinderplus-db/2024-10-22.1/AMR.LIB.h3p b/...amrfinderplus-db/2024-01-31.1/AMR.LIB.h3p → ...amrfinderplus-db/2024-10-22.1/AMR.LIB.h3p
diff --git a/test/db/amrfinderplus-db/2024-10-22.1/AMRProt-mutation.tsv b/test/db/amrfinderplus-db/2024-10-22.1/AMRProt-mutation.tsv
diff --git a/...nderplus-db/2024-01-31.1/AMRProt-suppress → ...plus-db/2024-10-22.1/AMRProt-suppress.tsv b/...nderplus-db/2024-01-31.1/AMRProt-suppress → ...plus-db/2024-10-22.1/AMRProt-suppress.tsv
@@ -1,4 +1,5 @@
 #taxgroup	protein_accession	protein_gi
+Burkholderia_mallei	ABN88303.1	126224798
 Escherichia	AAA21095.1	151858
 Escherichia	AAA21096.1	151859
 Escherichia	AAB09628.1	1061418

diff --git a/...s-db/2024-01-31.1/AMRProt-susceptible.tab → ...s-db/2024-10-22.1/AMRProt-susceptible.tsv b/...s-db/2024-01-31.1/AMRProt-susceptible.tab → ...s-db/2024-10-22.1/AMRProt-susceptible.tsv
diff --git a/...amrfinderplus-db/2024-01-31.1/AMRProt.pdb → ...finderplus-db/2024-10-22.1/AMRProt.fa.pdb b/...amrfinderplus-db/2024-01-31.1/AMRProt.pdb → ...finderplus-db/2024-10-22.1/AMRProt.fa.pdb
diff --git a/test/db/amrfinderplus-db/2024-10-22.1/AMRProt.fa.phr b/test/db/amrfinderplus-db/2024-10-22.1/AMRProt.fa.phr
diff --git a/test/db/amrfinderplus-db/2024-10-22.1/AMRProt.fa.pin b/test/db/amrfinderplus-db/2024-10-22.1/AMRProt.fa.pin
diff --git a/test/db/amrfinderplus-db/2024-10-22.1/AMRProt.fa.pjs b/test/db/amrfinderplus-db/2024-10-22.1/AMRProt.fa.pjs
@@ -0,0 +1,22 @@
+{
+  "version": "1.2",
+  "dbname": "AMRProt.fa",
+  "dbtype": "Protein",
+  "db-version": 5,
+  "description": "/tmp/amrfinder_index.e6b30A/db/AMRProt.fa",
+  "number-of-letters": 3040158,
+  "number-of-sequences": 8776,
+  "last-updated": "2024-10-30T14:36:00",
+  "number-of-volumes": 1,
+  "bytes-total": 4986731,
+  "bytes-to-cache": 3119271,
+  "files": [
+    "AMRProt.fa.pdb",
+    "AMRProt.fa.phr",
+    "AMRProt.fa.pin",
+    "AMRProt.fa.pot",
+    "AMRProt.fa.psq",
+    "AMRProt.fa.ptf",
+    "AMRProt.fa.pto"
+  ]
+}
diff --git a/...amrfinderplus-db/2024-01-31.1/AMRProt.psq → ...finderplus-db/2024-10-22.1/AMRProt.fa.psq b/...amrfinderplus-db/2024-01-31.1/AMRProt.psq → ...finderplus-db/2024-10-22.1/AMRProt.fa.psq
diff --git a/...amrfinderplus-db/2024-01-31.1/AMRProt.ptf → ...finderplus-db/2024-10-22.1/AMRProt.fa.ptf b/...amrfinderplus-db/2024-01-31.1/AMRProt.ptf → ...finderplus-db/2024-10-22.1/AMRProt.fa.ptf
diff --git a/...amrfinderplus-db/2024-01-31.1/AMR_CDS.nto → ...finderplus-db/2024-10-22.1/AMRProt.fa.pto b/...amrfinderplus-db/2024-01-31.1/AMR_CDS.nto → ...finderplus-db/2024-10-22.1/AMRProt.fa.pto
diff --git a/...amrfinderplus-db/2024-01-31.1/AMR_CDS.ndb → ...finderplus-db/2024-10-22.1/AMR_CDS.fa.ndb b/...amrfinderplus-db/2024-01-31.1/AMR_CDS.ndb → ...finderplus-db/2024-10-22.1/AMR_CDS.fa.ndb
diff --git a/test/db/amrfinderplus-db/2024-10-22.1/AMR_CDS.fa.nhr b/test/db/amrfinderplus-db/2024-10-22.1/AMR_CDS.fa.nhr
diff --git a/test/db/amrfinderplus-db/2024-10-22.1/AMR_CDS.fa.nin b/test/db/amrfinderplus-db/2024-10-22.1/AMR_CDS.fa.nin
diff --git a/test/db/amrfinderplus-db/2024-10-22.1/AMR_CDS.fa.njs b/test/db/amrfinderplus-db/2024-10-22.1/AMR_CDS.fa.njs
@@ -0,0 +1,22 @@
+{
+  "version": "1.2",
+  "dbname": "AMR_CDS.fa",
+  "dbtype": "Nucleotide",
+  "db-version": 5,
+  "description": "/tmp/amrfinder_index.e6b30A/db/AMR_CDS.fa",
+  "number-of-letters": 8685586,
+  "number-of-sequences": 8507,
+  "last-updated": "2024-10-30T14:36:00",
+  "number-of-volumes": 1,
+  "bytes-total": 4061483,
+  "bytes-to-cache": 2279672,
+  "files": [
+    "AMR_CDS.fa.ndb",
+    "AMR_CDS.fa.nhr",
+    "AMR_CDS.fa.nin",
+    "AMR_CDS.fa.not",
+    "AMR_CDS.fa.nsq",
+    "AMR_CDS.fa.ntf",
+    "AMR_CDS.fa.nto"
+  ]
+}
diff --git a/...amrfinderplus-db/2024-01-31.1/AMR_CDS.not → ...finderplus-db/2024-10-22.1/AMR_CDS.fa.not b/...amrfinderplus-db/2024-01-31.1/AMR_CDS.not → ...finderplus-db/2024-10-22.1/AMR_CDS.fa.not
diff --git a/...amrfinderplus-db/2024-01-31.1/AMR_CDS.nsq → ...finderplus-db/2024-10-22.1/AMR_CDS.fa.nsq b/...amrfinderplus-db/2024-01-31.1/AMR_CDS.nsq → ...finderplus-db/2024-10-22.1/AMR_CDS.fa.nsq
diff --git a/...amrfinderplus-db/2024-01-31.1/AMR_CDS.ntf → ...finderplus-db/2024-10-22.1/AMR_CDS.fa.ntf b/...amrfinderplus-db/2024-01-31.1/AMR_CDS.ntf → ...finderplus-db/2024-10-22.1/AMR_CDS.fa.ntf
diff --git a/...amrfinderplus-db/2024-01-31.1/AMRProt.pto → ...finderplus-db/2024-10-22.1/AMR_CDS.fa.nto b/...amrfinderplus-db/2024-01-31.1/AMRProt.pto → ...finderplus-db/2024-10-22.1/AMR_CDS.fa.nto
diff --git a/test/db/amrfinderplus-db/2024-10-22.1/database_format_version.txt b/test/db/amrfinderplus-db/2024-10-22.1/database_format_version.txt
@@ -0,0 +1 @@
+4.0.1
diff --git a/.../db/amrfinderplus-db/2024-01-31.1/fam.tab → .../db/amrfinderplus-db/2024-10-22.1/fam.tsv b/.../db/amrfinderplus-db/2024-01-31.1/fam.tab → .../db/amrfinderplus-db/2024-10-22.1/fam.tsv
diff --git a/...mrfinderplus-db/2024-01-31.1/taxgroup.tab → ...mrfinderplus-db/2024-10-22.1/taxgroup.tsv b/...mrfinderplus-db/2024-01-31.1/taxgroup.tab → ...mrfinderplus-db/2024-10-22.1/taxgroup.tsv
@@ -1,17 +1,20 @@
 #taxgroup	gpipe_taxgroup	number_of_nucl_ref_genes
 Acinetobacter_baumannii	Acinetobacter	1
 Burkholderia_cepacia	Burkholderia_cepacia_complex	0
+Burkholderia_mallei	Burkholderia_mallei	0
 Burkholderia_pseudomallei	Burkholderia_pseudomallei	0
 Campylobacter	Campylobacter	3
 Citrobacter_freundii	Citrobacter_freundii	0
-Clostridioides_difficile	Clostridioides_difficile	1
+Clostridioides_difficile	Clostridioides_difficile	2
+Corynebacterium_diphtheriae	Corynebacterium_diphtheriae	0
 Enterobacter_asburiae	Enterobacter_asburiae	0
 Enterobacter_cloacae	Enterobacter_cloacae	0
 Enterococcus_faecalis	Enterococcus_faecalis	1
 Enterococcus_faecium	Enterococcus_faecium	1
 Escherichia	Escherichia_coli_Shigella	6
+Haemophilus_influenzae	Haemophilus_influenzae	0
 Klebsiella_oxytoca	Klebsiella_oxytoca	1
-Klebsiella_pneumoniae	Klebsiella	0
+Klebsiella_pneumoniae	Klebsiella	1
 Neisseria_gonorrhoeae	Neisseria_gonorrhoeae	6
 Neisseria_meningitidis	Neisseria_meningitidis	0
 Pseudomonas_aeruginosa	Pseudomonas_aeruginosa	0

diff --git a/test/db/amrfinderplus-db/2024-10-22.1/version.txt b/test/db/amrfinderplus-db/2024-10-22.1/version.txt
@@ -0,0 +1 @@
+2024-10-22.1
diff --git a/test/db/amrfinderplus-db/latest b/test/db/amrfinderplus-db/latest
@@ -1 +1 @@
-2024-01-31.1
+2024-10-22.1