7adb1d36b6e6f5ce11d882f348af4b1194ad17b6
max
  Wed Apr 7 01:05:10 2021 -0700
comitting a few changes to the uniprot pipeline to make it more stable for ottomatization, but also to get the filters to work correctly, refs #27069

diff --git src/hg/utils/otto/uniprot/bed12UniProtFullSeqBgp.as src/hg/utils/otto/uniprot/bed12UniProtFullSeqBgp.as
new file mode 100644
index 0000000..0e85e61
--- /dev/null
+++ src/hg/utils/otto/uniprot/bed12UniProtFullSeqBgp.as
@@ -0,0 +1,48 @@
+table bed12BgpUniProtAnnot
+"Browser extensible data (12 fields), eight fields for bigGenePred support, plus extra fields (dbName-pmids, not used by all UniProt subtracks) with UniProt-specific information"
+    (
+    string chrom;      "Chromosome (or contig, scaffold, etc.)"
+    uint   chromStart; "Start position in chromosome"
+    uint   chromEnd;   "End position in chromosome"
+    string name;       "Name of item"
+    uint   score;      "Score from 0-1000"
+    char[1] strand;    "+ or -"
+    uint thickStart;   "Start of where display should be thick (start codon)"
+    uint thickEnd;     "End of where display should be thick (stop codon)"
+    uint reserved;     "Used as itemRgb as of 2004-11-22"
+    int blockCount;    "Number of blocks"
+    int[blockCount] blockSizes; "Comma separated list of block sizes"
+    int[blockCount] chromStarts; "Start positions relative to chromStart"
+
+    string name2;               "Alternative/human readable name"
+    string cdsStartStat;        "Status of CDS start annotation (none, unknown, incomplete, or complete)"
+    string cdsEndStat;          "Status of CDS end annotation (none, unknown, incomplete, or complete)"
+    int[blockCount] exonFrames; "Exon frame {0,1,2}, or -1 if no frame for exon"
+    string type;                "Transcript type"
+    string geneName;            "Primary identifier for gene"
+    string geneName2;           "Alternative/human-readable gene name"
+    string geneType;            "Gene type"
+
+    string acc; "UniProt main accession"
+    lstring uniprotName; "UniProt main record name"
+    string status; "UniProt status"
+    lstring accList; "UniProt all accessions"
+    lstring isoIds; "UniProt isoform accessions"
+
+    lstring protFullNames; "UniProt protein name"
+    lstring protShortNames; "UniProt protein short name"
+    lstring protAltFullNames; "UniProt alternative names"
+    lstring protAltShortNames; "UniProt alternative short names"
+    lstring geneNameDupl; "UniProt gene name"
+    lstring geneSynonyms; "UniProt gene synonyms"
+    lstring functionText; "UniProt function"
+
+    lstring hgncSym; "HGNC Gene Symbol"
+    lstring hgncId; "HGNC ID"
+    lstring refSeq; "RefSeq IDs"
+    lstring refSeqProt; "RefSeq Protein IDs"
+    lstring entrezGene; "NCBI Entrez Gene"
+    lstring ensGene; "Ensembl Gene IDs"
+    lstring ensTrans; "Ensembl Transcript IDs"
+    lstring ensProt; "Ensembl Protein IDs"
+    )