Updated file handling with new VMR on sheet 1 not 0

taxmyphage/download_check.py

@@ -141,7 +141,7 @@ def check_blastDB(
                 )
                 print_error("Will download the database now and create database")
 
-                url = "https://millardlab-inphared.s3.climb.ac.uk/Bacteriophage_genomes.fasta.gz"
+                url = "https://millardlab-taxmyphage.s3.climb.ac.uk/Bacteriophage_genomes_MSL39v1.fasta.gz"
 
                 create_folder(os.path.dirname(blastdb_path))
 
@@ -202,7 +202,7 @@ def check_mash_index(mash_index_path: str, install: bool = False) -> None:
             )
             print_error("Will download the database now and create database")
 
-            url = "https://millardlab-inphared.s3.climb.ac.uk/ICTV_2023.msh"
+            url = "https://millardlab-taxmyphage.s3.climb.ac.uk/ICTV_MSL39v1.msh"
 
             create_folder(os.path.dirname(mash_index_path))
 

taxmyphage/handle_files.py

@@ -101,8 +101,15 @@ def read_VMR(VMR_path: str) -> pd.DataFrame:
     Returns:
         pd.DataFrame: DataFrame containing the VMR data
     """
-
-    taxa_df = pd.read_excel(VMR_path, sheet_name=0)
+    #update to VMR means sheet posistion changes- change below to 1 or find automatically
+    #taxa_df = pd.read_excel(VMR_path, sheet_name=0)
+
+    excel_file = pd.ExcelFile(VMR_path)
+    sheet_names = excel_file.sheet_names
+    # Find the first sheet number that contains 'VMR'
+    vmr_sheet_index = next((index for index, sheet in enumerate(sheet_names) if 'VMR' in sheet), None)
+
+    taxa_df = pd.read_excel(VMR_path, sheet_name=vmr_sheet_index)
 
     # Print the DataFrame and rename a column
     # ic(taxa_df.head())

taxmyphage_results/Results_per_genome/UP30/Output_of_taxonomy.tsv

@@ -0,0 +1,26 @@
+genome	genus_cluster	species_cluster	Isolate ID	Species Sort	Isolate Sort	Realm	Subrealm	Kingdom	Subkingdom	Phylum	Subphylum	Class	Subclass	Order	Suborder	Family	Subfamily	Genus	Subgenus	Species	Exemplar or additional isolate	Virus name(s)	Virus name abbreviation(s)	Virus isolate designation	Genbank	Virus REFSEQ accession	Virus REFSEQ NCBI taxid	Genome coverage	Genome composition	Host source	Accessions Link
+MF093736	1	1	1001687.0	1271.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus ISF002	E	Shigella phage vB_SsoS-ISF002	Not Defined Yet	Not Defined Yet	MF093736	NC_041995	2006922	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+MG049919	1	1	1001686.0	1270.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus ISF001	E	Shigella phage vB_SflS-ISF001	Not Defined Yet	Not Defined Yet	MG049919	NC_047863	2048005	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+LC516895	1	2	1001684.0	1268.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus DELF2	E	Escherichia phage vB_EcoS-DELF2	Not Defined Yet	Not Defined Yet	LC516895	NC_049832	2697005	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+MZ501092	1	3	1024948.0	1274.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus leonhardeuler	E	Escherichia phage LeonhardEuler	LeonhardEuler	Not Defined Yet	MZ501092	Not Defined Yet	Not Defined Yet	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+KP085586	1	4	1001690.0	1277.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus PSf2	E	Shigella phage pSf-2	Not Defined Yet	Not Defined Yet	KP085586	NC_026010	1572702	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+MF468274	1	5	1001691.0	1282.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus Sfin1	E	Shigella phage Sfin-1	Not Defined Yet	Not Defined Yet	MF468274	NC_047998	2024314	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+KU194205	1	6	1001689.0	1273.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus JMPW2	E	Escherichia phage JMPW2	Not Defined Yet	Not Defined Yet	KU194205	NC_041873	1772218	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+AY216660	1	7	1001696.0	1287.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus T1	E	Escherichia phage T1	Not Defined Yet	Not Defined Yet	AY216660	NC_005833	2492962	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+OL960582	1	8	1024952.0	1279.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus SA12KD	E	Escherichia phage vB_EcoS_SA12KD	SA12KD	Not Defined Yet	OL960582	Not Defined Yet	Not Defined Yet	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+MH051911	1	9	1001685.0	1269.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus IME18	E	Enterobacteria phage vB_EcoS_IME18	Not Defined Yet	Not Defined Yet	MH051911	NC_047959	2163886	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+KY985004	1	10	1001693.0	1284.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus SH2	E	Escherichia phage vB_EcoS_SH2	Not Defined Yet	Not Defined Yet	KY985004	NC_047828	1983554	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+JX912252	1	11	1001682.0	1264.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus ADB2	E	Escherichia phage ADB-2	Not Defined Yet	Not Defined Yet	JX912252	NC_019725	1216926	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+HM035024	1	12	1001695.0	1286.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus Shfl1	E	Shigella phage Shfl1	Not Defined Yet	Not Defined Yet	HM035024	NC_015456	2919551	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+query_UP30	1	13	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet	Not Defined Yet
+OQ223306	1	14	1024951.0	1278.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus S202	E	Shigella phage S2_02	S2_02	Not Defined Yet	OQ223306	Not Defined Yet	Not Defined Yet	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+MT682715	1	15	1024946.0	1266.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus chapo	E	Escherichia phage vB_EcoS_Chapo	Chapo	Not Defined Yet	MT682715	Not Defined Yet	Not Defined Yet	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+OL960579	1	16	1024953.0	1280.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus SA30RD	E	Escherichia phage vB_EcoS_SA30RD	SA30RD	Not Defined Yet	OL960579	Not Defined Yet	Not Defined Yet	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+MN296515	1	17	1001692.0	1283.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus Sfin3	E	Shigella phage Sfin-3	Not Defined Yet	Not Defined Yet	MN296515	NC_049831	2848075	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+OP455115	1	18	1024950.0	1276.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus LHE71	E	Escherichia phage LHE71	LHE71	Not Defined Yet	OP455115	Not Defined Yet	Not Defined Yet	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+MH285980	1	19	1001683.0	1265.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus BIFF	E	Escherichia phage Eco_BIFF	Not Defined Yet	Not Defined Yet	MH285980	NC_047996	2175169	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+KX828710	1	20	1001694.0	1285.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus SH6	E	Shigella phage SH6	Not Defined Yet	Not Defined Yet	KX828710	NC_047785	1913048	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+OP094641	1	21	1024949.0	1275.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus Lg3	E	Escherichia phage Lg3	Lg3	Not Defined Yet	OP094641	Not Defined Yet	Not Defined Yet	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+OL960578	1	22	1024954.0	1281.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus SA32RD	E	Escherichia phage vB_EcoS_SA32RD	SA32RD	Not Defined Yet	OL960578	Not Defined Yet	Not Defined Yet	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+OL800706	1	23	1024947.0	1267.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus CLBP3	E	Escherichia phage CLB_P3	CLB_P3	Not Defined Yet	OL800706	Not Defined Yet	Not Defined Yet	Complete genome	dsDNA	bacteria	NCBI Nucleotide
+KU194206	1	24	1001688.0	1272.0	1.0	Duplodnaviria	Not Defined Yet	Heunggongvirae	Not Defined Yet	Uroviricota	Not Defined Yet	Caudoviricetes	Not Defined Yet	Not Defined Yet	Not Defined Yet	Drexlerviridae	Tunavirinae	Tunavirus	Not Defined Yet	Tunavirus JMPW1	E	Escherichia phage JMPW1	Not Defined Yet	Not Defined Yet	KU194206	NC_041874	1772219	Complete genome	dsDNA	bacteria	NCBI Nucleotide

taxmyphage_results/Results_per_genome/UP30/Summary_file.txt

@@ -0,0 +1,47 @@
+--------------- TAXMYPHAGE RESULTS ---------------
+
+Query sequence can be classified within a current genus and represents a new species, it is in:
+
+Class: Caudoviricetes
+Family: Drexlerviridae
+Subfamily: Tunavirinae
+Genus: Tunavirus
+Species: Tunavirus new_name
+
+-------------- INFORMATION MESSAGES --------------
+
+INFO: Current ICTV taxonomy and the clustering on genomic similarity algorithm output appear to be consistent at the genus level
+
+The data from the initial mash searching is below as tsv format
+
+/!\ Remember taxmyPHAGE compared against viruses classified by the ICTV. Allowing you determine if it represents a new species or genus.
+It does not tell you if it is similar to other phages that have yet to be classified.
+You can do this by comparison with INPHARED database if you wish https://github.com/RyanCook94/inphared or BLAST etc.
+
+------------------ MASH RESULTS ------------------
+
+Reference	Query	distance	p-value	shared-hashes	ANI
+./Tunavirus/HM035024.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0820539	0	490/5000	
+./Tunavirus/OL960578.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0836797	0	472/5000	
+./Tunavirus/MZ501092.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.083772	0	471/5000	
+./Tunavirus/MH051911.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0845181	0	463/5000	
+./Tunavirus/MN296515.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0847068	0	461/5000	
+./Tunavirus/KY985004.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0851824	0	456/5000	
+./Tunavirus/KP085586.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0854706	0	453/5000	
+./Tunavirus/OQ223306.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0859554	0	448/5000	
+./Tunavirus/LC516895.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0864461	0	443/5000	
+./Tunavirus/MH285980.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.087043	0	437/5000	
+./Tunavirus/MF093736.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0873447	0	434/5000	
+./Tunavirus/OL960579.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0880576	0	427/5000	
+./Tunavirus/KU194206.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0880576	0	427/5000	
+./Tunavirus/JX912252.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0901662	0	407/5000	
+./Tunavirus/KX828710.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0901662	0	407/5000	
+./Tunavirus/MF468274.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0903831	0	405/5000	
+./Tunavirus/OP455115.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0903831	0	405/5000	
+./Tunavirus/OL800706.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0914855	0	395/5000	
+./Tunavirus/KU194205.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0936649	0	376/5000	
+./Tunavirus/MT682715.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0936649	0	376/5000	
+./Tunavirus/OP094641.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0940198	0	373/5000	
+./Tunavirus/OL960582.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0943778	0	370/5000	
+./Tunavirus/AY216660.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.0985328	0	337/5000	
+./Tunavirus/MG049919.fna	/home/andrew/tax_myPHAGE/taxmyphage_results/Results_per_genome/UP30/query.fasta	0.108654	0	269/5000