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/bigPslUniprot.as src/hg/utils/otto/uniprot/bigPslUniprot.as
new file mode 100644
index 0000000..308024b
--- /dev/null
+++ src/hg/utils/otto/uniprot/bigPslUniprot.as
@@ -0,0 +1,57 @@
+table bigPsl
+"bigPsl pairwise alignment"
+    (
+    string chrom;       "Reference sequence chromosome or scaffold"
+    uint   chromStart;  "Start position in chromosome"
+    uint   chromEnd;    "End position in chromosome"
+    string name;        "Name or ID of item, ideally both human readable and unique"
+    uint score;         "Score (0-1000)"
+    char[1] strand;     "+ or - indicates whether the query aligns to the + or - strand on the reference"
+    uint thickStart;    "Start of where display should be thick (start codon)"
+    uint thickEnd;      "End of where display should be thick (stop codon)"
+    uint reserved;       "RGB value (use R,G,B string in input file)"
+    int blockCount;     "Number of blocks"
+    int[blockCount] blockSizes; "Comma separated list of block sizes"
+    int[blockCount] chromStarts; "Start positions relative to chromStart"
+
+    uint    oChromStart;"Start position in other chromosome"
+    uint    oChromEnd;  "End position in other chromosome"
+    char[1] oStrand;    "+ or -, - means that psl was reversed into BED-compatible coordinates" 
+    uint    oChromSize; "Size of other chromosome."
+    int[blockCount] oChromStarts; "Start positions relative to oChromStart or from oChromStart+oChromSize depending on strand"
+
+    lstring  oSequence;  "Sequence on other chrom (or edit list, or empty)"
+    string   oCDS;       "CDS in NCBI format"
+
+    uint    chromSize;"Size of target chromosome"
+
+    uint match;        "Number of bases matched."
+    uint misMatch; " Number of bases that don't match "
+    uint repMatch; " Number of bases that match but are part of repeats "
+    uint nCount;   " Number of 'N' bases "
+    uint seqType;    "0=empty, 1=nucleotide, 2=amino_acid"
+
+    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 geneName; "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"
+    )
+