Added pretiosus

lmc297 · Jun 1, 2023 · f20c6ad · f20c6ad
1 parent 8f3b532
commit f20c6ad
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diff --git a/btyper3/__init__.py b/btyper3/__init__.py
@@ -417,7 +417,7 @@ def main():
 
 	parser.add_argument("--ani_geneflow", help = "Optional argument; True or False; assign genome to a pseudo-gene flow unit using the method described by Carroll, et al. using FastANI; default = False", nargs = "?", default = "False")
 
-	parser.add_argument("--ani_typestrains", help = "Optional argument; True or False; calculate ANI values between the query genome relative to all B. cereus s.l. species type strain genomes using FastANI, and report the closest species type strain/highest ANI value; default = False", nargs = "?", default = "False")
+	parser.add_argument("--ani_typestrains", help = "Optional argument; True or False; calculate ANI values between the query genome relative to all B. cereus s.l. species type strain genomes using FastANI, and report the closest species type strain/highest ANI value; default = True", nargs = "?", default = "True")
 
 	parser.add_argument("--virulence", help = "Optional argument; True or False; perform virulence gene detection (required if one wants to assign genomes to biovars Anthracis or Emeticus); default = True", nargs = "?", default = "True")
 

diff --git a/btyper3/seq_ani_db/typestrains/typestrains.tsv b/btyper3/seq_ani_db/typestrains/typestrains.tsv
@@ -18,6 +18,7 @@ B_pacificus_EB422_GCF_001884025.fna.gz	pacificus	https://ftp.ncbi.nlm.nih.gov/ge
 B_paramobilis_BML-BC017_GCF_018332495.fna.gz	paramobilis	https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/332/495/GCF_018332495.1_ASM1833249v1/GCF_018332495.1_ASM1833249v1_genomic.fna.gz
 B_paramycoides_NH24A2_GCF_001884235.fna.gz	paramycoides	https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/884/235/GCF_001884235.1_ASM188423v1/GCF_001884235.1_ASM188423v1_genomic.fna.gz
 B_paranthracis_Mn5_GCF_001883995.fna.gz	paranthracis	https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/883/995/GCF_001883995.1_ASM188399v1/GCF_001883995.1_ASM188399v1_genomic.fna.gz
+B_pretiosus_SAICEU11T_GCF_025916425.fna.gz	pretiosus	https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/025/916/425/GCF_025916425.1_ASM2591642v1/GCF_025916425.1_ASM2591642v1_genomic.fna.gz
 B_proteolyticus_TD42_GCF_001884065.fna.gz	proteolyticus	https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/884/065/GCF_001884065.1_ASM188406v1/GCF_001884065.1_ASM188406v1_genomic.fna.gz
 B_pseudomycoides_DSM_12442_GCF_000161455.fna.gz	pseudomycoides	https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/161/455/GCF_000161455.1_ASM16145v1/GCF_000161455.1_ASM16145v1_genomic.fna.gz
 B_rhizoplanae_CIP_111899_GCF_917563915.fna.gz	rhizoplanae	https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/917/563/915/GCF_917563915.1_JJ-63/GCF_917563915.1_JJ-63_genomic.fna.gz