f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f
jcasper
  Wed Mar 6 11:33:33 2024 -0800
Updates for new uniProt import, refs #30476

diff --git src/hg/protein/spToDb/spDbTables.as src/hg/protein/spToDb/spDbTables.as
index 72b6cca..9b53e6f 100644
--- src/hg/protein/spToDb/spDbTables.as
+++ src/hg/protein/spToDb/spDbTables.as
@@ -1,261 +1,261 @@
 table displayId
 "Relate ID and primary accession. A good table to use just get handle on all records."
     (
-    char[12] acc;	"Primary accession"
-    char[12] val;	"SwissProt display ID"
+    char[20] acc;	"Primary accession"
+    char[24] val;	"SwissProt display ID"
     )
 
 table otherAcc
 "Relate ID and other accessions"
     (
-    char[12] acc;	"Primary accession"
+    char[20] acc;	"Primary accession"
     char[12] val;	"Secondary accession"
     )
 
 table organelle
 "A part of a cell that has it's own genome"
     (
     int id;	"Organelle ID - we create this"
     lstring val;	"Text description"
     )
 
 table info
 "Small stuff with at most one copy associated with each SwissProt record"
     (
-    char[12] acc;	"Primary accession"
+    char[20] acc;	"Primary accession"
     byte isCurated;	"True if curated (SwissProt rather than trEMBL)"
     int aaSize;		"Size in amino acids"
     int molWeight;	"Molecular weight"
     string createDate;	"Creation date"
     string seqDate;	"Sequence last update date"
     string annDate;	"Annotation last update date"
     int organelle;	"Pointer into organelle table"
     )
 
 table description
 "Description lines"
     (
-    char[12] acc;	"Primary accession"
+    char[20] acc;	"Primary accession"
     lstring val; 	"SwissProt DE lines"
     )
 
 table geneLogic
 "Gene including and/or logic if multiple"
     (
-    char[12] acc;	"Primary accession"
+    char[20] acc;	"Primary accession"
     lstring val;	"Gene(s) and logic to relate them."
     )
 
 table gene
 "Gene/accession relationship. Both sides can be multiply valued."
     (
-    char[12] acc;	"Primary accession"
+    char[20] acc;	"Primary accession"
     string val;		"Single gene name"
     byte isPrimary;	"True if primary gene name, false if a synonym"
     )
 
 table taxon
 "An NCBI taxon"
     (
     int id;		"Taxon NCBI ID"
     string binomial;	"Binomial format name"
     lstring toGenus;	"Taxonomy - superkingdom to genus"
     )
 
 table commonName
 "Common name for a taxon"
     (
     int taxon;	"Taxon table ID"
     string val; "Common name"
     )
 
 table accToTaxon
 "accession/taxon relationship"
     (
-    char[12] acc;	"Primary accession"
+    char[20] acc;	"Primary accession"
     int	taxon;		"ID in taxon table"
     )
 
 table pathogenHost
 "Host of pathogenic organism"
     (
     int pathogen;  "Pathogen taxon"
     int host;	   "Host taxon"
     )
 
 table keyword
 "A keyword"
     (
     int id;	"Keyword ID - we create this"
     string val;	"Keyword itself"
     )
 
 table accToKeyword
 "Relate keywords and accessions"
     (
-    char[12] acc;	"Primary accession"
+    char[20] acc;	"Primary accession"
     int keyword;	"ID in keyword table"
     )
 
 table commentType
 "A type of comment"
     (
     int id;	"Comment type ID, we create this"
     string val;	"Name of comment type"
     )
 
 table commentVal
 "Text of a comment"
     (
     int id;	"Comment value ID - we create this"
     lstring val;	"Text of comment."
     )
 
 table comment
 "A structured comment"
     (
-    char[12] acc;     "Primary accession"
+    char[20] acc;     "Primary accession"
     int commentType; "ID in commentType table"
     int commentVal;  "ID in commentVal table"
     )
 
 table protein
 "Amino acid sequence"
     (
-    char[12] acc;	"Primary accession"
+    char[20] acc;	"Primary accession"
     lstring val;	"Amino acids"
     )
 
 table extDb
 "Name of another database"
     (
     int id;	"Database id - we make this up"
     string val;	"Name of database"
     )
 
 table extDbRef
 "A reference to another database"
     (
-    char[12] acc;	"Primary SwissProt accession"
+    char[20] acc;	"Primary SwissProt accession"
     int extDb;		"ID in extDb table"
     string extAcc1;	"External accession"
     string extAcc2;	"External accession"
     string extAcc3;	"External accession"
     )
 
 table featureClass
 "A class of feature"
     (
     int id;	"Database id - we make this up"
     string val;	"Name of class"
     )
 
 table featureType
 "A type of feature"
     (
     int id;	"Database id - we make this up"
     lstring val;	"Name of type"
     )
 
 table feature
 "A description of part of a protein"
     (
-    char[12] acc;	"Primary accession"
+    char[20] acc;	"Primary accession"
     int start;	"Start coordinate (zero based)"
     int end;	"End coordinate (non-inclusive)"
     int featureClass;	"ID of featureClass"
     int featureType;    "ID of featureType"
     ushort softEndBits;  "1 for start <, 2 for start ?, 4 for end >, 8 for end ?"
     )
 
 table author
 "A single author"
     (
     int id;	"ID of this author"
     string val;	"Name of author"
     )
 
 table reference
 "An article (or book or patent) in literature."
     (
     int id;	"ID of this reference"
     lstring title; "Title"
     lstring cite; "Enough info to find journal/patent/etc."
     string pubMed; "Pubmed cross-reference"
     string medline; "Medline cross-reference"
     )
 
 table referenceAuthors
 "This associates references and authors"
     (
     int reference;	"ID in reference table"
     int author;		"ID in author table"
     )
 
 table citationRp
 "SwissProt RP (Reference Position) line.  Often includes reason for citing."
     (
     int id;	"ID of this citationRp"
     lstring val;	"Reason for citing/position in sequence of cite."
     )
 
 table citation
 "A SwissProt citation of a reference"
     (
     int id;		"ID of this citation"
-    char[12] acc;	"Primary accession"
+    char[20] acc;	"Primary accession"
     int reference;	"ID in reference table"
     int rp;		"ID in rp table"
     )
 
 table rcType
 "Types found in a swissProt reference RC (reference comment) line"
     (
     int id;	"ID of this one"
     string val; "name of this"
     )
 
 table rcVal
 "Values found in a swissProt reference RC (reference comment) line"
     (
     int id;	"ID of this"
     lstring val; "associated text"
     )
 
 table citationRc
 "Reference comments associated with citation"
     (
     int citation;	"ID in citation table"
     int rcType;		"ID in rcType table"
     int rcVal;		"ID in rcVal table"
     )
 
 table varProtein
 "Contains just the variably spliced proteins"
     (
-    char[12] acc;	"Primary accession"
+    char[20] acc;	"Primary accession of variant"
     lstring val;	"Amino acids"
     )
 
 table varAcc
 "Accessions and other info on the variably-spliced proteins"
     (
-    char[12] varAcc;	"Accession of variant"
-    char[12] parAcc;    "Accession of parent (non-variant)"
-    char[4] variant;    "Variant part of accession"
+    char[20] varAcc;	"Accession of variant"
+    char[20] parAcc;    "Accession of parent (non-variant)"
+    char[5] variant;    "Variant part of accession"
     )
 
 table proteinEvidenceType
 "Type of evidence that this is actually a protein"
     (
     int id;	"ID of type (shared with UniProt)"
     lstring val; "Description of protein evidence"
     )
 
 table proteinEvidence
 "Associate protein with evidence for its existence"
     (
-    char[12] acc;	"Primary accession"
+    char[20] acc;	"Primary accession"
     int proteinEvidenceType;	"ID in proteinEvidenceType table"
     )