Merge branch 'development'

klebgenomics · Aug 18, 2021 · cf10096 · cf10096
2 parents 718317c + 9854c72
commit cf10096
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diff --git a/images/ybt_tree_jun2021.png b/images/ybt_tree_jun2021.png
diff --git a/kleborate/data/AbST_profiles.txt b/kleborate/data/AbST_profiles.txt
@@ -62,3 +62,34 @@ ST	iucA	iucB	iucC	iucD	iutA	iuc_lineage
 61	45	24	33	35	61	iuc 5
 62	45	12	33	35	61	iuc 5
 63	1	15	1	1	1	iuc 1
+64	9	7	12	13	17	iuc 3
+65	1	1	15	1	1	iuc 1
+66	45	21	33	39	24	iuc 5
+67	51	1	39	1	37	iuc 1
+68	51	1	40	1	38	iuc 1
+69	12	29	42	34	13	iuc 3
+70	52	33	12	8	34	iuc 3
+71	12	14	42	38	30	iuc 3
+72	12	30	22	37	33	iuc 3
+73	12	30	22	37	31	iuc 3
+74	12	30	22	37	32	iuc 3
+75	1	1	1	1	36	iuc 1
+76	1	1	41	1	1	iuc 1
+77	1	1	1	33	1	iuc 1
+78	1	1	34	1	1	iuc 1
+79	9	34	38	8	9	iuc 3
+80	9	7	12	8	35	iuc 3
+81	9	35	12	8	17	iuc 3
+82	52	7	12	8	17	iuc 3
+83	52	33	12	8	17	iuc 3
+84	53	2	13	2	26	iuc 2
+85	12	14	22	36	51	iuc 3
+86	12	30	22	37	13	iuc 3
+87	12	31	22	37	13	iuc 3
+88	25	9	25	31	52	iuc 3
+89	25	9	45	23	52	iuc 3
+90	25	9	43	23	39	iuc 3
+91	25	9	25	31	40	iuc 3
+92	25	36	25	31	52	iuc 3
+93	25	9	44	31	52	iuc 3
+94	45	12	33	35	22	iuc 5
diff --git a/kleborate/data/CbST_profiles.txt b/kleborate/data/CbST_profiles.txt
@@ -63,4 +63,16 @@ ST	clbA	clbB	clbC	clbD	clbE	clbF	clbG	clbH	clbI	clbL	clbM	clbN	clbO	clbP	clbQ	cl
 62	5	10	2	2	2	4	2	8	2	2	2	2	2	2	2	clb 3
 63	5	21	2	2	2	4	2	8	2	2	2	2	2	2	2	clb 3
 64	6	10	2	2	2	2	2	17	2	2	2	2	2	2	2	clb 3
-65	7	6	1	3	1	3	1	6	3	1	8	16	14	1	1	clb 1
+65	7	6	1	3	1	3	1	6	3	1	8	16	14	1	1	clb 1
+66	1	65	1	1	1	3	1	25	3	1	1	1	14	1	1	clb 1
+67	1	15	6	1	1	3	5	6	3	1	1	24	5	1	1	clb 1
+68	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	clb 2
+69	8	10	21	2	2	2	2	28	2	2	2	2	2	2	2	clb 3
+70	1	66	1	1	9	3	1	6	23	1	1	25	16	1	1	clb 1
+71	2	68	2	2	2	2	2	2	2	2	2	2	2	2	2	clb 2
+72	9	2	2	2	2	2	2	3	2	2	2	2	2	2	2	clb 2
+73	2	10	21	2	2	2	2	28	2	2	2	2	2	2	2	clb 3
+74	1	67	1	1	1	3	10	25	3	1	1	26	14	1	1	clb 1
+75	1	13	1	1	1	3	5	6	6	1	1	27	4	1	1	clb 1
+76	1	7	1	1	1	3	1	6	3	1	1	1	3	12	1	clb 1
+77	2	69	2	2	2	2	2	3	2	2	2	2	2	2	2	clb 2
diff --git a/kleborate/data/ICEKp_references/ICEKp15.gff b/kleborate/data/ICEKp_references/ICEKp15.gff
diff --git a/kleborate/data/ICEKp_references/ICEKp16.gff b/kleborate/data/ICEKp_references/ICEKp16.gff
diff --git a/kleborate/data/ICEKp_references/ICEKp17.gff b/kleborate/data/ICEKp_references/ICEKp17.gff
diff --git a/kleborate/data/ICEKp_references/ICEKp18.gff b/kleborate/data/ICEKp_references/ICEKp18.gff
diff --git a/kleborate/data/ICEKp_references/ICEKp19.gff b/kleborate/data/ICEKp_references/ICEKp19.gff
diff --git a/kleborate/data/ICEKp_references/ICEKp20.gff b/kleborate/data/ICEKp_references/ICEKp20.gff
diff --git a/kleborate/data/ICEKp_references/ICEKp21.gff b/kleborate/data/ICEKp_references/ICEKp21.gff
diff --git a/kleborate/data/ICEKp_references/ICEKp22.gff b/kleborate/data/ICEKp_references/ICEKp22.gff
diff --git a/kleborate/data/Klebsiella_pneumoniae.fasta b/kleborate/data/Klebsiella_pneumoniae.fasta
diff --git a/kleborate/data/SmST_profiles.txt b/kleborate/data/SmST_profiles.txt
@@ -1,36 +1,49 @@
 ST	iroB	iroC	iroD	iroN	iro_lineage
-34	23	48	17	19	iro 5
-35	23	49	18	20	iro 5
-7	6	19	10	5	iro 3
-11	6	14	8	6	iro 3
-17	6	19	11	16	iro 3
-18	21	39	19	5	iro 3
-21	6	38	10	5	iro 3
-25	6	19	11	5	iro 3
-28	6	18	10	5	iro 3
-32	6	36	11	5	iro 3
+1	1	1	1	1	iro 1
+2	1	4	1	1	iro 1
 3	2	3	2	2	iro 2
 4	4	25	5	9	iro 2
 5	4	21	5	9	iro 2
 6	4	9	13	4	iro 2
-9	7	16	9	8	iro 2
-12	2	34	2	2	iro 2
-20	4	21	5	18	iro 2
-22	4	9	5	4	iro 2
-26	16	34	2	2	iro 2
-27	9	22	2	10	iro 2
-33	22	33	12	15	iro 4
-1	1	1	1	1	iro 1
-2	1	4	1	1	iro 1
+7	6	19	10	5	iro 3
 8	1	8	1	1	iro 1
+9	7	16	9	8	iro 2
 10	1	13	1	1	iro 1
+11	6	14	8	6	iro 3
+12	2	34	2	2	iro 2
 13	1	15	1	7	iro 1
 14	1	1	1	3	iro 1
 15	1	1	3	1	iro 1
 16	1	37	1	1	iro 1
+17	6	19	11	16	iro 3
+18	21	39	19	5	iro 3
 19	1	2	1	1	iro 1
+20	4	21	5	18	iro 2
+21	6	38	10	5	iro 3
+22	4	9	5	4	iro 2
 23	1	30	1	14	iro 1
 24	1	20	1	1	iro 1
+25	6	19	11	5	iro 3
+26	16	34	2	2	iro 2
+27	9	22	2	10	iro 2
+28	6	18	10	5	iro 3
 29	10	4	1	1	iro 1
 30	1	27	1	1	iro 1
-31	1	28	1	1	iro 1
+31	1	28	1	1	iro 1
+32	6	36	11	5	iro 3
+33	22	33	12	15	iro 4
+34	23	48	17	19	iro 5
+35	23	49	18	20	iro 5
+36	9	22	2	26	iro 2
+37	4	25	5	30	iro 2
+38	23	52	21	19	iro 5
+39	31	59	25	29	iro 5
+40	1	1	1	31	iro 1
+41	1	58	1	1	iro 1
+42	1	1	1	32	iro 1
+43	1	56	9	1	iro 1
+44	1	57	26	1	iro 1
+45	1	4	1	33	iro 1
+46	2	3	2	34	iro 2
+47	23	60	18	20	iro 5
+48	32	16	9	8	iro 2