BigDataBiology · luispedro · Apr 25, 2024 · Apr 21, 2024 · Apr 21, 2024 · Apr 22, 2024
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/manual_curation/README.md b/argnorm/data/manual_curation/README.md
@@ -0,0 +1,21 @@
+# Resfinder Notes
+
+## Gene Clusters
+
+- Resfinder has gene clusters (nucleotide sequence with multiple CDSs present) which can't be passed through RGI using 'contig' mode.
+- Gene clusters were identified and were manually assigned ARO numbers.
+- 40 gene clusters present.
+
+## Reverse Complement
+1) blaBIM-1_1_CP016446
+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
+
+- 9 genes in reverse complement form also present.
+- RC genes were manually curated
diff --git a/argnorm/data/manual_curation/resfinder_curation.tsv b/argnorm/data/manual_curation/resfinder_curation.tsv
@@ -1,3 +1,50 @@
-Original ID	ARO
-EstDL136_1_JN242251	
-aac(3)-I_1_AJ877225	3007384
+Original ID	Gene Name in CARD	ARO	Origin	Position in Cluster	Description
+VanHAX_1_FJ866609	glycopeptide resistance gene cluster VanA	3000236	https://www.ncbi.nlm.nih.gov/nuccore/M97297.1?report=fasta	6018-8624	"Part of VanA cluster (ARO:3000236). Contains: ARO:3002942, ARO:3000010, and ARO:3002949 "
+VanHAX_2_M97297	glycopeptide resistance gene cluster VanA	3000236	https://www.ncbi.nlm.nih.gov/nuccore/FJ866609?report=fasta	3762-6368	"Part of VanA cluster (ARO:3000236). Contains: ARO:3002942 and ARO:3002949. The vanA gene (ARO:3002949) is modified, 1 G substituded with 1 T  "
+VanHMX_1_FJ349556	glycopeptide resistance gene cluster VanM	3000256	https://www.ncbi.nlm.nih.gov/nuccore/FJ349556.1?report=fasta	3884-6502	"Part of VanM cluster (ARO:3000256). Contains: ARO: ARO:3002947, ARO:3002911, and ARO:3002953"
+vanM_1_FJ349556	glycopeptide resistance gene cluster VanM	3000256	https://www.ncbi.nlm.nih.gov/nuccore/FJ349556.1?report=fasta	Whole Cluster	"full vanM cluster, ARO:3000256"
+VanC1XY_1_AF162694	glycopeptide resistance gene cluster VanC	3000246	https://www.ncbi.nlm.nih.gov/nuccore/AF162694.1?report=fasta	1411-3011	"Part of VanC cluster (ARO:3000246). Contains: ARO:3000368, ARO:3002966"
+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)
+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
+VanHBX_1_AF192329	glycopeptide resistance gene cluster VanB	3000238	https://www.ncbi.nlm.nih.gov/nuccore/AF192329	27871-30477	Part of VanB cluster (ARO:3000238)
+VanHBX_2_U35369	glycopeptide resistance gene cluster VanB	3000238	https://www.ncbi.nlm.nih.gov/nuccore/U35369.1?report=fasta	4007-6613	"Part of VanB cluster (ARO:3000238). Contains ARO:3002943, ARO:3002950"
+VanC4XY_1_EU151752	glycopeptide resistance gene cluster VanC	3000246	https://www.ncbi.nlm.nih.gov/nuccore/EU151752.1?report=fasta	29-1650	Part of VanC cluster (ARO:3000246)
+VanC4XY_2_EU151753	glycopeptide resistance gene cluster VanC	3000246	https://www.ncbi.nlm.nih.gov/nuccore/EU151753.1?report=fasta	29-1650	Part of VanC cluster (ARO:3000246)
+VanC2XY_2_EU151755	glycopeptide resistance gene cluster VanC	3000246	https://www.ncbi.nlm.nih.gov/nuccore/EU151755.1?report=fasta	29-1650	Part of VanC cluster (ARO:3000246)
+VanC4XY_3_EU151756	glycopeptide resistance gene cluster VanC	3000246	https://www.ncbi.nlm.nih.gov/nuccore/EU151756.1?report=fasta	29-1650	Part of VanC cluster (ARO:3000246)
+VanC2XY_3_EU151757	glycopeptide resistance gene cluster VanC	3000246	https://www.ncbi.nlm.nih.gov/nuccore/EU151757.1?report=fasta	29-1650	Part of VanC cluster (ARO:3000246)
+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_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)
+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"
+VanG2XY_1_FJ872410	glycopeptide resistance gene cluster VanG	3000257	https://www.ncbi.nlm.nih.gov/nuccore/FJ872410	39328-41138	Part of VanG cluster (ARO:3000257)
+VanLXY_1_EU250284	glycopeptide resistance gene cluster VanL	3000260	https://www.ncbi.nlm.nih.gov/nuccore/EU250284.1?report=fasta	955-2578	"Part of VanL cluster (ARO:3000260). Contains ARO:3002910, ARO:3002968"
+VanNXY_1_JF802084	glycopeptide resistance gene cluster VanN	3002917	https://www.ncbi.nlm.nih.gov/nuccore/JF802084.2?report=fasta	560-2165	"Part of VanN cluster (ARO:3002917). Contains ARO:3002912, ARO:3002969"
+VanHOX_1_KF478993	glycopeptide resistance gene cluster VanO	3002918	https://www.ncbi.nlm.nih.gov/nuccore/KF478993.1?report=fasta	491-3185	"Part of VanO cluster (ARO:3002918). Contains ARO:3002948, ARO:3002954"
+vanXmurFvanWI_1_CP001336	glycopeptide resistance gene cluster VanI	3003722	https://www.ncbi.nlm.nih.gov/nuccore/CP001336.1?report=fasta	1776504-1780580	Part of VanI cluster (ARO:300372). Origin has both VanI cluster and VanB cluster. Contains ARO:3003725
+vanXmurFvanKWI_1_NZAGAF01000127	glycopeptide resistance gene cluster VanI	3003722	https://www.ncbi.nlm.nih.gov/nuccore/NZ_AGAF01000127.1?report=fasta	3324-8562	Part of VanI cluster (ARO:300372). CDS in origin is in reverse complement form.
+vanXmurFvanKWI_2_AP008230	glycopeptide resistance gene cluster VanI	3003722	https://www.ncbi.nlm.nih.gov/nuccore/AP008230.1?report=fasta	4202889-4208186	Part of VanI cluster (ARO:300372). Contains ARO:3003727
+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.
+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.
+blaSPG-1_1_KP109680	SPG-1	3003720
+blaBIM-1_1_CP016446	BlaB	3004201
+grdA_1_QJX10702
+aac(3)-I_1_AJ877225	AAC(3)-I	3007384
+EstDL136_1_JN242251