Vdjdb skills and massive update

.gitignore

@@ -1,6 +1,8 @@
+.claude/
 tmp/
 database/
 !database/dummy
+patches/*.pdf
 
 ## Groovy / Java
 

chunks/PDB_Database.txt

@@ -258,7 +258,7 @@ chunk.id	cdr3.alpha	v.alpha	j.alpha	cdr3.beta	v.beta	d.beta	j.beta	species	mhc.a
 257	CAGNTGTASKLTF	TRAV12-2*01	TRAJ44*01	CASSGLAGGPVSGANVLTF	TRBV9*01		TRBJ2-6*01	HomoSapiens	HLA-A*03:01	B2M	MHCI	ALHGGWTTK	PIK3CA	Homo sapiens	https://github.com/antigenomics/vdjdb-db/issues/215																	7l1d	
 258	CALSGGTSYGKLTF	TRAV9-2*01	TRAJ52*01	CASSQGQDTEAFF	TRBV7-3*01		TRBJ1-1*01	HomoSapiens	HLA-DQA1*05	HLA-DQB1*02	MHCII	QPFPQPEQPFP	DQ2-GLIA-OMEGA1	Homo sapiens	https://github.com/antigenomics/vdjdb-db/issues/215																	7sg0	
 259	CLVGGLARDMRF	TRAV4*01	TRAJ43*01	CSVALGSDTGELFF	TRBV29-1*01		TRBJ2-2*01	HomoSapiens	HLA-DQA1*05	HLA-DQB1*02	MHCII	LQPFPQPELPYGSGGS	DQ2-GLIA-OMEGA1	Homo sapiens	https://github.com/antigenomics/vdjdb-db/issues/215																	7sg1	
-260	CLVGGLARDMRF	TRAV4*01	TRAJ43*01 	CSVALGSDTGELFF	TRBV29-1*01		TRBJ2-2*01	HomoSapiens	HLA-DQA1*05	HLA-DQB1*02	MHCII	LQPFPQPELPYGSGGS	DQ2-GLIA-OMEGA1	Homo sapiens	https://github.com/antigenomics/vdjdb-db/issues/215																	7sg2	
+260	CLVGGLARDMRF	TRAV4*01	TRAJ43*01	CSVALGSDTGELFF	TRBV29-1*01		TRBJ2-2*01	HomoSapiens	HLA-DQA1*05	HLA-DQB1*02	MHCII	LQPFPQPELPYGSGGS	DQ2-GLIA-OMEGA1	Homo sapiens	https://github.com/antigenomics/vdjdb-db/issues/215																	7sg2	
 261	CLVGGAYTGGFKTIF	TRAV4*01	TRAJ9*01	CASSLVAETYEQYF	TRBV11-2*01		TRBJ2-7*01	HomoSapiens	HLA-A*03:01	B2M	MHCI	ALHGGWTTK	PIK3CA	HomoSapiens	https://github.com/antigenomics/vdjdb-db/issues/215																	7rrg	
 262	CAVSLGTGAGSYQLTF	TRAV21	TRAJ28	CASSVGLYSTDTQYF	TRBV9		TRBJ2-3	HomoSapiens	HLA-B*27:05	B2M	MHCI	TRLALIAPK	PRPF3	HomoSapiens	PMID:36477533	antigen-loaded-targets		yes	amplicon-seq	tetramer-stain				Ankylosing Spondylitis			AS3.1		synovial fluid			7n2s	
 263	CAVLSPVQETSGSRLTF	TRAV21	TRAJ58	CASSVGLFSTDTQYF	TRBV9		TRBJ2-3	HomoSapiens	HLA-B*27:05	B2M	MHCI	TRLALIAPK	PRPF3	HomoSapiens	PMID:36477533	antigen-loaded-targets		yes	amplicon-seq	tetramer-stain				Ankylosing Spondylitis			AS4.2		synovial fluid			7n2n	

chunks/PMID_15589168.txt

@@ -1610,7 +1610,7 @@ chunk.id	cdr3.alpha	v.alpha	j.alpha	cdr3.beta	v.beta	d.beta	j.beta	species	mhc.a
 1609	CVLRPGVNNLF	TRAV22						MacacaMulatta	Mamu-A*01	B2M	MHCI	TTPESANL	Tat	SIV	PMID:15589168	tetramer-sort	2/100		sanger						887	5wk						
 1610	CVLRRDDKII	TRAV22						MacacaMulatta	Mamu-A*01	B2M	MHCI	TTPESANL	Tat	SIV	PMID:15589168	tetramer-sort	2/100		sanger						887	5wk						
 1611	CVLSINYKYI	TRAV22						MacacaMulatta	Mamu-A*01	B2M	MHCI	TTPESANL	Tat	SIV	PMID:15589168	tetramer-sort	2/100		sanger						887	5wk						
-1612	CAVKGSGGSYQKVT	TRAV23						MacacaMulatta	Mamu-A*01	B2M	MHCI	TTPESANL	Tat	SIV	PMID:15589168	tetramer-sort	2/100		sanger						887	5wk						
+1612	CAVKGSGGSYQKVT	TRAV23/DV6						MacacaMulatta	Mamu-A*01	B2M	MHCI	TTPESANL	Tat	SIV	PMID:15589168	tetramer-sort	2/100		sanger						887	5wk						
 1613	CATNASSNTGKLI	TRAV3						MacacaMulatta	Mamu-A*01	B2M	MHCI	TTPESANL	Tat	SIV	PMID:15589168	tetramer-sort	14/100		sanger						895	5wk						
 1614	CAVRNNNDRVI	TRAV13						MacacaMulatta	Mamu-A*01	B2M	MHCI	TTPESANL	Tat	SIV	PMID:15589168	tetramer-sort	14/100		sanger						895	5wk						
 1615	CVLKEGGNNRLA	TRAV22						MacacaMulatta	Mamu-A*01	B2M	MHCI	TTPESANL	Tat	SIV	PMID:15589168	tetramer-sort	12/100		sanger						895	5wk						

chunks/PMID_15596521.txt

@@ -1,18 +1,18 @@
 chunk.id	cdr3.alpha	v.alpha	j.alpha	cdr3.beta	v.beta	d.beta	j.beta	species	mhc.a	mhc.b	mhc.class	antigen.epitope	antigen.gene	antigen.species	reference.id	method.identification	method.frequency	method.singlecell	method.sequencing	method.verification	meta.study.id	meta.cell.subset	meta.subset.frequency	meta.subject.cohort	meta.subject.id	meta.replica.id	meta.clone.id	meta.epitope.id	meta.tissue	meta.donor.MHC	meta.donor.MHC.method	meta.structure.id
 1	CIVRAPGRADMR	TRAV26-1	TRAJ43	CASSYLPGQGDHYSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKEKGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	005				PBMC	HLA-A*02:01,HLA-A*24:02;HLA-B*08:01,HLA-B*5701;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*07:01,HLA-DRB*13:01		
 2				CASSFEAGQGFFSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKEKGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	065				PBMC	HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1		
-3	CAVPSGAGSYQLT	TRAV23	TRAJ28	CASSFEPGQGFYSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKEKGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	200				PBMC	HLA-A*02,HLA-A*24:02;HLA-B*08:01,HLA-B*15;HLA-Cw*07,HLA-Cw*12;HLA-DRB*13:01,HLA-DRB*03:01		
+3	CAVPSGAGSYQLT	TRAV23/DV6	TRAJ28	CASSFEPGQGFYSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKEKGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	200				PBMC	HLA-A*02,HLA-A*24:02;HLA-B*08:01,HLA-B*15;HLA-Cw*07,HLA-Cw*12;HLA-DRB*13:01,HLA-DRB*03:01		
 4	CAVKASGSRLT	TRAV2-1	TRAJ58	CASSYEPGQVSHYSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKEKGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	046				PBMC	HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1		
 5	CAYRPPGTYKYI	TRAV14-1	TRAJ40	CASSALASLNEQF	TRBV14		TRBJ2-1	HomoSapiens	HLA-B*08	B2M	MHCI	FLKEKGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	046				PBMC	HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1		
 6	CIVRAPGRADMR	TRAV26-1	TRAJ43	CASSYLPGQGDHYSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKEQGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	005				TCL culture	HLA-A*02:01,HLA-A*24:02;HLA-B*08:01,HLA-B*5701;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*07:01,HLA-DRB*13:01		
 7				CASSFEAGQGFFSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKEQGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	065				TCL culture	HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1		
-8	CAVPSGAGSYQLT	TRAV23	TRAJ28	CASSFEPGQGFYSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKEQGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	200				TCL culture	HLA-A*02,HLA-A*24:02;HLA-B*08:01,HLA-B*15;HLA-Cw*07,HLA-Cw*12;HLA-DRB*13:01,HLA-DRB*03:01		
+8	CAVPSGAGSYQLT	TRAV23/DV6	TRAJ28	CASSFEPGQGFYSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKEQGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	200				TCL culture	HLA-A*02,HLA-A*24:02;HLA-B*08:01,HLA-B*15;HLA-Cw*07,HLA-Cw*12;HLA-DRB*13:01,HLA-DRB*03:01		
 9	CAVKASGSRLT	TRAV2-1	TRAJ58	CASSYEPGQVSHYSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKEQGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	046				TCL culture	HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1		
 10	CIVRAPGRADMR	TRAV26-1	TRAJ43	CASSYLPGQGDHYSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKETGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	005				TCL culture	HLA-A*02:01,HLA-A*24:02;HLA-B*08:01,HLA-B*5701;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*07:01,HLA-DRB*13:01		
 11				CASSFEAGQGFFSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKETGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	065				TCL culture	HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1		
-12	CAVPSGAGSYQLT	TRAV23	TRAJ28	CASSFEPGQGFYSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKETGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	200				TCL culture	HLA-A*02,HLA-A*24:02;HLA-B*08:01,HLA-B*15;HLA-Cw*07,HLA-Cw*12;HLA-DRB*13:01,HLA-DRB*03:01		
+12	CAVPSGAGSYQLT	TRAV23/DV6	TRAJ28	CASSFEPGQGFYSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKETGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	200				TCL culture	HLA-A*02,HLA-A*24:02;HLA-B*08:01,HLA-B*15;HLA-Cw*07,HLA-Cw*12;HLA-DRB*13:01,HLA-DRB*03:01		
 13	CAVKASGSRLT	TRAV2-1	TRAJ58	CASSYEPGQVSHYSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKETGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	046				TCL culture	HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1		
 14	CIVRAPGRADMR	TRAV26-1	TRAJ43	CASSYLPGQGDHYSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKEMGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	005				TCL culture	HLA-A*02:01,HLA-A*24:02;HLA-B*08:01,HLA-B*5701;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*07:01,HLA-DRB*13:01		
 15				CASSFEAGQGFFSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKEMGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	065				TCL culture	HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1		
-16	CAVPSGAGSYQLT	TRAV23	TRAJ28	CASSFEPGQGFYSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKEMGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	200				TCL culture	HLA-A*02,HLA-A*24:02;HLA-B*08:01,HLA-B*15;HLA-Cw*07,HLA-Cw*12;HLA-DRB*13:01,HLA-DRB*03:01		
+16	CAVPSGAGSYQLT	TRAV23/DV6	TRAJ28	CASSFEPGQGFYSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKEMGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	200				TCL culture	HLA-A*02,HLA-A*24:02;HLA-B*08:01,HLA-B*15;HLA-Cw*07,HLA-Cw*12;HLA-DRB*13:01,HLA-DRB*03:01		
 17	CAVKASGSRLT	TRAV2-1	TRAJ58	CASSYEPGQVSHYSNQPQH	TRBV13-2		TRBJ1-5	HomoSapiens	HLA-B*08	B2M	MHCI	FLKEMGGL	Nef	HIV-1	PMID:15596521	tetramer-sort			sanger	antigen-loaded-targets		CD8+		HIV+	046				TCL culture	HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1