ENH: Use amino acid version of resfinder database

- Resfinder is comprised of coding sequences. The data wasn't being handled properly before as contig mode was used when passing coding sequences to RGI. Now, the amino acid versions of Resfinder is used with protein mode when running the database in RGI. - Resfinder AA file is generated using biopython from nucleotide file (AA file not found online). - 9 RC genes were found (previously 4 were found). All were manually curated as RC versions couldn't be translated properly into AA sequences. - Documentation updated in changelog to reflect AA version being used for Resfinder and gene cluster handling
BigDataBiology · Apr 22, 2024 · 3cb8dec · 3cb8dec
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -35,11 +35,21 @@
 
 ## Unreleased
 
-### Using amino acid file for argannot rather than nucleotide file
-- ARG-ANNOT is comprised of coding sequences. The data wasn't being handled properly before as contig mode was used when passing coding sequences to RGI. Now, the amino acid version of ARG-ANNOT is used with protein mode when running the database in RGI.
-- One to many ARO mapping such as NG_047831:101-955 to Erm(K) and almG eliminated as protein mode used
-- A total of 10 ARO mappings changed
-### argnorm.lib: Making argNorm more usable as a library 
+### Handling gene clusters & reverse complements in resfinder
+- Resfinder has gene clusters which can't be passed through RGI using 'contig' mode.
+- Gene clusters were identified and were manually assigned ARO numbers.
+- A seperate file with manual curation for gene clusters and RCs was created, and their AROs were updated after concatenating RGI results and genes not in RGI results.
+- 40 gene clusters present.
+- 9 genes in reverse complement form also present.
+- RC genes were manually curated.
+
+### Using amino acid file for argannot & resfinder rather than nucleotide file
+- ARG-ANNOT and Resfinder are comprised of coding sequences. The data wasn't being handled properly before as contig mode was used when passing coding sequences to RGI. Now, the amino acid versions of ARG-ANNOT & Resfinder are used with protein mode when running the database in RGI.
+- ARG-ANNOT AA file is available online. Resfinder AA file is generated using biopython.
+- One to many ARO mapping such as NG_047831:101-955 to Erm(K) and almG in ARG-ANNOT eliminated as protein mode used
+- A total of 10 ARO mappings changed in ARG-ANNOT
+
+### argnorm.lib: Making argNorm more usable as a library
 - A file called `lib.py` will be introduced so that users can use argNorm as a library more easily.
 - Users can import the `map_to_aro` function using `from argnorm.lib import map_to_aro`. The function takes a gene name as input, maps the gene to the ARO and returns a pronto term object with the ARO mapping.
 - The `get_aro_mapping_table` function, previously within the BaseNormalizer class, has also been moved to `lib.py` to give users the ability to access the mapping tables being used for normalization.

diff --git a/argnorm/data/cluster_rc_correction/notes.md b/argnorm/data/cluster_rc_correction/notes.md
@@ -10,11 +10,11 @@
 2) blaSPG-1_1_KP109680
 3) grdA_1_QJX10702
 4) tet(43)_1_GQ244501
+5) aac(3)-Xa_1_AB028210
+6) blaBKC-1_1_KP689347
+7) mph(A)_1_D16251
+8) qepA1_1_AB263754
+9) aac(3)-I_1_AJ877225
 
-
-- 4 genes in reverse complement form also present.
-- blaBIM-1_1_CP016446 and mph(D)_1_AB048591 were not found in CARD and were given parent ARO mappings.
-- RGI correctly assigned ARO numbers to other two.
-
-# erm(X)_1_M36726
-- Had one to many ARO mapping due to include loose. Included correct ARO number for it.
+- 9 genes in reverse complement form also present.
+- RC genes were manually curated
diff --git a/argnorm/data/cluster_rc_correction/resfinder_cluster_rc_correction.tsv b/argnorm/data/cluster_rc_correction/resfinder_cluster_rc_correction.tsv
@@ -7,7 +7,6 @@ VanC1XY_1_AF162694	glycopeptide resistance gene cluster VanC	3000246	https://www
 VanC1XY_2_DQ022190	glycopeptide resistance gene cluster VanC	3000246	https://www.ncbi.nlm.nih.gov/nuccore/DQ022190.1?report=fasta	205-1805	Part of VanC cluster (ARO:3000246).
 VanC2XY_1_EU151754	glycopeptide resistance gene cluster VanC	3000246	https://www.ncbi.nlm.nih.gov/nuccore/EU151754.1?report=fasta	29-1650	Part of VanC cluster (ARO:3000246)
 VanHAX_PT_1_DQ018710	glycopeptide resistance gene cluster VanA	3000236	https://www.ncbi.nlm.nih.gov/nuccore/DQ018710.1	5109-7715	Part of VanA cluster (ARO:3000236)
-grdA_1_QJX10702			https://www.ncbi.nlm.nih.gov/nuccore/MT246861.1?report=fasta	3023-3529	Part of plasmid. No ARO found. Nucleotides in reverse complement form in resfinder db.
 VanHAX_PA_1_DQ018711	glycopeptide resistance gene cluster VanA	3000236	https://www.ncbi.nlm.nih.gov/nuccore/DQ018711.1?report=fasta	3168-5750	Part of VanA cluster (ARO:3000236)
 VanHAX_PT_2_AY926880	glycopeptide resistance gene cluster VanA	3000236	https://www.ncbi.nlm.nih.gov/nuccore/AY926880.2?report=fasta	2771-5377	Part of VanA cluster (ARO:3000236)
 dldHA2X_1_AL939117			https://www.ncbi.nlm.nih.gov/nuccore/AL939117.1	53343-56013	Gene not in CARD
@@ -21,13 +20,13 @@ VanC2XY_3_EU151757	glycopeptide resistance gene cluster VanC	3000246	https://www
 VanC2XY_4_EU151758	glycopeptide resistance gene cluster VanC	3000246	https://www.ncbi.nlm.nih.gov/nuccore/EU151758.1?report=fasta	29-1650	Part of VanC cluster (ARO:3000246)
 VanC3XY_2_EU151759	glycopeptide resistance gene cluster VanC	3000246	https://www.ncbi.nlm.nih.gov/nuccore/EU151759.1?report=fasta	29-1650	Part of VanC cluster (ARO:3000246)
 VanC2XY_5_EU151760	glycopeptide resistance gene cluster VanC	3000246	https://www.ncbi.nlm.nih.gov/nuccore/EU151760.1?report=fasta	29-1650	Part of VanC cluster (ARO:3000246)
-VanHDX_6_DQ172830	glycopeptide resistance gene cluster VanD	3000253	https://www.ncbi.nlm.nih.gov/nuccore/DQ172830.1?report=fasta	3019-5628	Part of VanD cluster (ARO:3000253) 
-VanHDX_7_AB242319	glycopeptide resistance gene cluster VanD	3000253	https://www.ncbi.nlm.nih.gov/nuccore/AB242319.1?report=fasta	3045-5654	Part of VanD cluster (ARO:3000253) 
-VanHDX_3_AF175293	glycopeptide resistance gene cluster VanD	3000253	https://www.ncbi.nlm.nih.gov/nuccore/AF175293.1?report=fasta	3115-5724	Part of VanD cluster (ARO:3000253) 
+VanHDX_6_DQ172830	glycopeptide resistance gene cluster VanD	3000253	https://www.ncbi.nlm.nih.gov/nuccore/DQ172830.1?report=fasta	3019-5628	Part of VanD cluster (ARO:3000253)
+VanHDX_7_AB242319	glycopeptide resistance gene cluster VanD	3000253	https://www.ncbi.nlm.nih.gov/nuccore/AB242319.1?report=fasta	3045-5654	Part of VanD cluster (ARO:3000253)
+VanHDX_3_AF175293	glycopeptide resistance gene cluster VanD	3000253	https://www.ncbi.nlm.nih.gov/nuccore/AF175293.1?report=fasta	3115-5724	Part of VanD cluster (ARO:3000253)
 VanHDX_4_AY082011	glycopeptide resistance gene cluster VanD	3000253	https://www.ncbi.nlm.nih.gov/nuccore/AY082011.1?report=fasta	4937-7546	"Part of VanD cluster (ARO:3000253). Contains ARO:3002944, ARO:3000005, ARO:3003070"
 VanHDX_5_AY489045	glycopeptide resistance gene cluster VanD	3000253	https://www.ncbi.nlm.nih.gov/nuccore/AY489045.1?report=fasta	3046-5655	Part of VanD cluster (ARO:3000253)
-VanHDX_1_AF130997	glycopeptide resistance gene cluster VanD	3000253	https://www.ncbi.nlm.nih.gov/nuccore/AF130997.1?report=fasta	3122-5728	Part of VanD cluster (ARO:3000253) 
-VanHDX_2_EU999036	glycopeptide resistance gene cluster VanD	3000253	https://www.ncbi.nlm.nih.gov/nuccore/EU999036.1?report=fasta	3044-5653	Part of VanD cluster (ARO:3000253) 
+VanHDX_1_AF130997	glycopeptide resistance gene cluster VanD	3000253	https://www.ncbi.nlm.nih.gov/nuccore/AF130997.1?report=fasta	3122-5728	Part of VanD cluster (ARO:3000253)
+VanHDX_2_EU999036	glycopeptide resistance gene cluster VanD	3000253	https://www.ncbi.nlm.nih.gov/nuccore/EU999036.1?report=fasta	3044-5653	Part of VanD cluster (ARO:3000253)
 VanHFX_1_AF155139	glycopeptide resistance gene cluster VanF	3000255	https://www.ncbi.nlm.nih.gov/nuccore/AF155139.2?report=fasta	4979-7648	"Part of VanF cluster (ARO:3000255). Contains ARO:3002945, ARO:3002908, ARO:3002952"
 VanEXY_1_FJ872411	glycopeptide resistance gene cluster VanE	3000259	https://www.ncbi.nlm.nih.gov/nuccore/FJ872411.1?report=fasta	39736-41347	"Part of VanE cluster (ARO:3000259). Contains ARO:3002907, ARO:3002967"
 VanGXY_1_AY271782	glycopeptide resistance gene cluster VanG	3000257	https://www.ncbi.nlm.nih.gov/nuccore/AY271782.1?report=fasta	21049-22859	"Part of VanG cluster (ARO:3000257). Contains ARO:3002909, ARO:3003069"
@@ -41,4 +40,8 @@ vanXmurFvanKWI_2_AP008230	glycopeptide resistance gene cluster VanI	3003722	http
 blaBIM-1_1_CP016446	BlaB	3004201	https://www.ncbi.nlm.nih.gov/nuccore/CP016446.1?report=fasta		Gene not in CARD. Reverse complement in resfinder db. Parent ARO used
 blaSPG-1_1_KP109680	SPG-1	3003720	https://www.ncbi.nlm.nih.gov/nuccore/KP109680.1?report=fasta	1255-2112	Reverse complement in resfinder db and origin.
 mph(D)_1_AB048591	macrolide phosphotransferase (MPH)	3000333	https://www.ncbi.nlm.nih.gov/nuccore/AB048591.1?report=fasta	4-840	Gene not in CARD. Parent ARO used.
-erm(X)_1_M36726	ErmX	3000596			
+aac(3)-Xa_1_AB028210	AAC(3)-Xa	3002544			Reverse complement in resfinder db.
+blaBKC-1_1_KP689347	BKC-1	3004757			Reverse complement in resfinder db.
+mph(A)_1_D16251	mphA	3000316			Reverse complement in resfinder db.
+qepA1_1_AB263754	QepA2	3004103			Reverse complement in resfinder db.
+tet(43)_1_GQ244501	tet(43)	3000573			Reverse complement in resfinder db.
diff --git a/argnorm/data/manual_curation/resfinder_curation.tsv b/argnorm/data/manual_curation/resfinder_curation.tsv
@@ -1,3 +1,6 @@
-Original ID	ARO
-EstDL136_1_JN242251	
-aac(3)-I_1_AJ877225	3007384
+Original ID	ARO	Gene Name in CARD
+blaSPG-1_1_KP109680	3003720	SPG-1
+blaBIM-1_1_CP016446	3004201	BlaB
+grdA_1_QJX10702		
+aac(3)-I_1_AJ877225	3007384	AAC(3)-I
+EstDL136_1_JN242251