Updating some Yersinia taxid (#16)

* Add files via upload

* adding taxonomy_v3.5.1

src/Kalamari_v3.9.1.tsv

@@ -0,0 +1,294 @@
+scientificName	nuccoreAcc	taxid
+Acholeplasma laidlawii	CP000896	2148
+Acinetobacter baumannii	CU468230	509170
+Acinetobacter pittii	NC_016603	48296
+Aeromonas hydrophila	NC_008570	644
+Agrobacterium fabrum	NC_003062	1176649
+Agrobacterium fabrum	NC_003063	1176649
+Alkaliphilus transvaalensis	CP000724	208226
+Aliivibrio fischeri	NC_006841	668
+Aliivibrio fischeri	NC_006840	668
+Amycolatopsis mediterranei	NC_014318	33910
+Aquifex aeolicus	NC_000918	63363
+Architeuthis dux	NC_011581	256136
+Arcobacter bivalviorum	CP031217	663364
+Arcobacter cibarius	XXXXXX	255507
+Arcobacter cloacae	XXXXXX	1054034
+Arcobacter cryaerophilus	XXXXXX	28198
+Arcobacter ellisii	CP032097	913109
+Arcobacter halophilus	CP031218	197482
+Arcobacter molluscorum	CP032098	1032072
+Arcobacter mytili	CP031219	603050
+Arcobacter skirrowii	XXXXXX	28200
+Arcobacter suis	CP032100	1278212
+Arcobacter thereius	XXXXXX	544718
+Arcobacter trophiarum	CP031367	708186
+Arcobacter venerupis	XXXXXX	1054033
+Arripis trutta	AP006810	270544
+Bacillus cereus	NC_016771	1396
+Bacillus subtilis	NC_000964	1423
+Bacillus thuringiensis	NC_005957	1428
+Bacteroides fragilis	NC_006347	817
+Bacteroides thetaiotaomicron	NC_004663	818
+Bartonella bacilliformis	CP000524	774
+Betacoronavirus coronavirus	MT233526	2697049
+Bifidobacterium bifidum	NC_014638	1681
+Bifidobacterium longum	NC_004307	216816
+Bordetella bronchiseptica	NC_019382	518
+Borreliella burgdorferi	NC_001318	139
+Bos taurus	KC153975	9913
+Brachybacterium faecium	NC_013172	43669
+Bradyrhizobium diazoefficiens	NC_004463	1355477
+Brassica oleracea	NC_016118	3712
+Buchnera aphidicola	NC_002528	9
+Burkholderia pseudomallei	NC_006350	28450
+Burkholderia pseudomallei	NC_006351	28450
+Campylobacter avium	CP022347	522484
+Campylobacter canadensis	XXXXXX	449520
+Campylobacter coli	XXXXXX	195
+Campylobacter concisus	CP012541	199
+Campylobacter cuniculorum	CP020867	374106
+Campylobacter fetus	CP006833	196
+Campylobacter gracilis	CP012196	824
+Campylobacter helveticus	NZ_CP020478	28898
+Campylobacter hyointestinalis hyointestinalis	CP015575	91352
+Campylobacter hyointestinalis lawsonii	CP015575	91353
+Campylobacter insulaenigrae	CP007770	260714
+Campylobacter jejuni	NC_002163	197
+Campylobacter lanienae	CP015578	75658
+Campylobacter lari	CP000932	201
+Campylobacter mucosalis	XXXXXX	202
+Campylobacter peloridis	CP007766	488546
+Campylobacter rectus	XXXXXX	203
+Campylobacter showae	XXXXXX	204
+Campylobacter sputorum	CP019683	202
+Campylobacter subantarcticus	CP007772	497724
+Campylobacter upsaliensis	XXXXXX	28080
+Campylobacter ureolyticus	CP012195	827
+Campylobacter volucris	CP007774	1031542
+Candidatus Desulforudis audaxviator	CP000860	471827
+Candidatus Korarchaeum cryptofilum	CP000968	374847
+Caulobacter	CP000927	366602
+Caulobacter vibrioides	NC_011916	155892
+Chlamydia pneumoniae	NC_000922	83558
+Chlamydia trachomatis	NC_000117	813
+Chlamydomonas reinhardtii	AF008237	3055
+Chlorobaculum tepidum	NC_002932	1097
+Chloroflexus aurantiacus	NC_010175	1108
+Citrobacter freundii	CP007557	1333848
+Clavibacter michiganensis_sepedonicus	AM849034	31964
+Clostridioides difficile	NC_009089	1496
+Clostridium acetobutylicum	NC_003030	1488
+Clostridium argentinense	CP014176	29341
+Clostridium baratii	CP014204	1561
+Clostridium botulinum groupI	NC_010723	9000005
+Clostridium botulinum groupII	NC_010516	9000004
+Clostridium butyricum	CP013239	1492
+Clostridium perfringens	NC_008262	1502
+Corynebacterium glutamicum	NC_003450	1718
+Corynebacterium urealyticum	AM942444	43771
+Coxiella burnetii	NC_002971	777
+Cronobacter condimenti	CP012264	1163710
+Cronobacter dublinensis dublinensis	CP012266	413498
+Cronobacter malonaticus	CP006731	413503
+Cronobacter muytjensii	CP012268	413501
+Cronobacter sakazakii	CP011047	28141
+Cronobacter turicensis	FN543093	413502
+Cronobacter universalis	CP012257	535744
+Cryptosporidium parvum	CM000429	353152
+Cryptosporidium parvum	CM000430	353152
+Cryptosporidium parvum	CM000431	353152
+Cryptosporidium parvum	CM000432	353152
+Cryptosporidium parvum	CM000433	353152
+Cryptosporidium parvum	CM000434	353152
+Cryptosporidium parvum	CM000435	353152
+Cryptosporidium parvum	CM000436	353152
+Cryptosporidium hominis	LN877947	237895
+Cryptosporidium hominis	LN877948	237895
+Cryptosporidium hominis	LN877949	237895
+Cryptosporidium hominis	LN877950	237895
+Cryptosporidium hominis	LN877951	237895
+Cryptosporidium hominis	LN877952	237895
+Cryptosporidium hominis	LN877953	237895
+Cryptosporidium hominis	LN877954	237895
+Cupriavidus taiwanensis	CU633750	164546
+Cupriavidus taiwanensis	CU633749	164546
+Cyanothece	CP000806	43989
+Deinococcus radiodurans	NC_001263	1299
+Delftia acidovorans	CP000884	80866
+Desulfovibrio vulgaris	NC_002937	881
+Dictyoglomus turgidum	NC_011661	513050
+Enterobacter cloacae	NC_014121	550
+Enterococcus faecalis	NC_004668	1351
+Enterococcus faecium	NC_017960	1352
+Escherichia albertii	XXXXXX	208962
+Escherichia coli	XXXXXX	83334
+Escherichia fergusonii	XXXXXX	564
+Escherichia hermanii	XXXXXX	565
+Escherichia vulneris	XXXXXX	566
+Exiguobacterium antarcticum	XXXXXX	132920
+Finegoldia magna	AP008971	1260
+Flavobacterium psychrophilum	NC_009613	96345
+Francisella philomiragia	CP000937	28110
+Francisella tularensis	NC_006570	263
+Fusobacterium nucleatum	NC_003454	851
+Gallus gallus	HQ857211	9031
+Gardnerella vaginalis	NC_014644	2702
+Geobacter sulfurreducens	NC_002939	35554
+Gloeobacter violaceus	NC_005125	33072
+Grimontia hollisae	XXXXXX	673
+Grimontia hollisae	XXXXXX	673
+Haemophilus influenzae	NC_000907	727
+Haemophilus somnus	CP000947	228400
+Halobacterium salinarum	AM774415	478009
+Helianthus annuus	MG770607	4232
+Helicobacter pylori	NC_000915	210
+Heliobacterium modesticaldum	CP000930	35701
+Homo sapiens	NC_012920	9606
+Ketogulonicigenium vulgare	NC_017384	92945
+Klebsiella aerogenes	NC_015663	548
+Klebsiella pneumoniae	NC_016845	573
+Lactobacillus acidophilus	NC_006814	1579
+Lactobacillus paracasei	NC_008526	1597
+Lactobacillus plantarum	NC_004567	1590
+Lactobacillus salivarius	NC_007929	1624
+Lactococcus lactis	NC_002662	1358
+Lactuca sativa	MK820672	75943
+Legionella pneumophila	NC_002942	446
+Leptospira biflexa	CP000777	355278
+Leptospira interrogans	NC_004342	173
+Leptothrix cholodnii	CP001013	34029
+Leuconostoc citreum	DQ489736	349519
+Listeria grayi	XXXXXX	1641
+Listeria innocua	XXXXXX	1642
+Listeria ivanovii	FR687253	1638
+Listeria marthii	CM001047	529731
+Listeria monocytogenes I	XXXXXX	9000000
+Listeria monocytogenes II	XXXXXX	9000001
+Listeria monocytogenes III	CP001175	9000002
+Listeria monocytogenes IV	XXXXXX	9000003
+Listeria seeligeri	XXXXXX	1640
+Listeria welshimeri	XXXXXX	1643
+Lysinibacillus sphaericus	CP000817	444177
+Mesoplasma florum	NC_006055	2151
+Mesorhizobium ciceri	NC_014923	39645
+Methylobacterium	CP000943	426117
+Methylobacterium radiotolerans	CP001001	31998
+Micrococcus luteus	CP001628	1270
+Moorella thermoacetica	NC_007644	1525
+Morganella morganii morganii	CP004345	180434
+Mycobacterium abscessus	NC_010397	36809
+Mycobacterium leprae	NC_002677	1769
+Mycobacterium smegmatis	NC_008596	1772
+Mycobacterium tuberculosis	NC_000962	1773
+Mycoplasma mycoides	NC_005364	2102
+Mycoplasma pneumoniae	NC_000912	2104
+Neisseria gonorrhoeae	NC_002946	485
+Neisseria meningitidis	NC_003112	487
+Neomysis japonica	KR006340	1676841
+Ochrobactrum anthropi	CP000758	529
+Ochrobactrum anthropi	CP000759	529
+Pantoea ananatis	CP001875	553
+Parabacteroides distasonis	CP000140	823
+Photobacterium damselae	XXXXXX	38293
+Photobacterium damselae	XXXXXX	38293
+Pollachius virens	FR751399	8060
+Polynucleobacter necessarius	CP001010	576610
+Prochlorococcus marinus	NC_005042	1219
+Proteus mirabilis	NC_022000	584
+Pseudomonas aeruginosa	NC_002516	287
+Pseudomonas putida	CP000949	390235
+Pseudomonas syringae group genomosp. 3	NC_004578	251701
+Pyrobaculum neutrophilum	CP001014	70771
+Rhodobacter sphaeroides	NC_007494	1063
+Rhodobacter sphaeroides	NC_007493	1063
+Rhodopirellula baltica	NC_005027	265606
+Rhodospirillum rubrum	NC_007643	1085
+Ruminococcus sp.	CP039381	1263
+Rickettsia prowazekii	NC_000963	782
+Salinibacter ruber	NC_007677	146919
+Salmonella bongori	FR877557	54736
+Salmonella enterica_IIa	XXXXXX	9000010
+Salmonella enterica_IIb	XXXXXX	9000011
+Salmonella enterica_IIIa	XXXXXX	9000014
+Salmonella enterica_IIIb	XXXXXX	9000015
+Salmonella enterica_I	AE006468	59201
+Salmonella enterica_IV	XXXXXX	59205
+Salmonella enterica_IX	XXXXXX	9000016
+Salmonella enterica_VII	XXXXXX	59208
+Salmonella enterica_VIII	XXXXXX	9000009
+Salmonella enterica_VI	XXXXXX	59207
+Salmonella enterica_X	XXXXXX	9000017
+Serratia liquefaciens	CP006252	614
+Shewanella halifaxensis	CP000931	271098
+Shewanella oneidensis	NC_004347	70863
+Shewanella woodyi	CP000961	60961
+Shimwellia blattae	CP001560	563
+Sinorhizobium fredii	NC_012587	380
+Sinorhizobium medicae	NC_009636	110321
+Sinorhizobium meliloti	NC_003047	382
+Solanum lycopersicum	NC_035963	4081
+Staphylococcus aureus	NZ_CP009554	46170
+Staphylococcus epidermidis	NC_004461	1282
+Streptococcus agalactiae	NC_004116	1311
+Streptococcus mitis	NC_013853	28037
+Streptococcus mutans	NC_004350	1309
+Streptococcus pneumoniae	CP000936	487214
+Streptococcus pyogenes	NC_002737	1314
+Streptococcus sanguinis	NC_009009	1305
+Streptococcus suis	NC_012926	1307
+Streptomyces coelicolor	NC_003888	1902
+Sus scrofa	FJ236999	9823
+Synechococcus	CP000951	32049
+Thermanaerovibrio acidaminovorans	NC_013522	81462
+Thermoanaerobacter pseudethanolicus	CP000924	496866
+Thermodesulfovibrio yellowstonii	NC_011296	28262
+Thermosynechococcus elongatus	NC_004113	146786
+Thermotoga maritima	NC_000853	2336
+Thermus thermophilus	NC_006461	274
+Thunnus alalunga	AB101291	8235
+Treponema denticola	NC_002967	158
+Ureaplasma parvum	CP000942	134821
+Vibrio alginolyticus	CP035699	663
+Vibrio alginolyticus	CP035700	663
+Vibrio cholerae_O1	CP038178	127906
+Vibrio cholerae_O1	CP038179	127906
+Vibrio cidicii	XXXXXX	1763883
+Vibrio cidicii	XXXXXX	1763883
+Vibrio cincinnatiensis	XXXXXX	675
+Vibrio cincinnatiensis	XXXXXX	675
+Vibrio fluvialis	XXXXXX	676
+Vibrio fluvialis	XXXXXX	676
+Vibrio furnissii	XXXXXX	29494
+Vibrio furnissii	XXXXXX	29494
+Vibrio harveyi	CP035692	669
+Vibrio harveyi	CP035693	669
+Vibrio metoecus	XXXXXX	1481663
+Vibrio metoecus	XXXXXX	1481663
+Vibrio metschnikovii	CP035684	28172
+Vibrio metschnikovii	CP035685	28172
+Vibrio mimicus	XXXXXX	674
+Vibrio mimicus	XXXXXX	674
+Vibrio navarrensis	XXXXXX	29495
+Vibrio navarrensis	XXXXXX	29495
+Vibrio parahaemolyticus	XXXXXX	670
+Vibrio parahaemolyticus	XXXXXX	670
+Vibrio vulnificus	XXXXXX	672
+Vibrio vulnificus	XXXXXX	672
+Vicia faba	KC189947	3906
+Xanthomonas campestris	NC_003902	339
+Xylella fastidiosa	CP000941	405440
+Yersinia aldovae	XXXXXX	29483
+Yersinia bercovieri	XXXXXX	634
+Yersinia canariae	NZ_CP043727	2607663
+Yersinia enterocolitica	NC_015224	630
+Yersinia enterocolitica	NC_008800	630
+Yersinia hibernica	NZ_CP032487	2339259
+Yersinia frederiksenii	XXXXXX	29484
+Yersinia intermedia	XXXXXX	631
+Yersinia intermedia	XXXXXX	631
+Yersinia mollaretii	XXXXXX	33060
+Yersinia pseudotuberculosis	CP000950	502800
+Yersinia pseudotuberculosis	NC_010465.1	502800
+Yersinia rochesterensis	CP032482	1604335
+Yersinia rohdei	CP009787	29485