643fc5346b9416e784bdf9b169ae9405d651264d
hiram
  Thu Jul 30 15:37:45 2026 -0700
definitions to load the assembly_summary files from NCBI refs #37958

diff --git src/hg/lib/assemblySummary.as src/hg/lib/assemblySummary.as
new file mode 100644
index 00000000000..a670add923f
--- /dev/null
+++ src/hg/lib/assemblySummary.as
@@ -0,0 +1,42 @@
+table assemblySummary
+"NCBI assembly_summary data, see: https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/README_assembly_summary.txt"
+    (
+    string assemblyAccession;	"www.ncbi.nlm.nih.gov/assembly/?term=xxx"
+    string bioproject;	"www.ncbi.nlm.nih.gov/bioproject/?term=xxx"
+    string biosample;	"www.ncbi.nlm.nih.gov/biosample/?term=xxx"
+    string wgsMaster;	"www.ncbi.nlm.nih.gov/nuccore/xxx"
+    string refseqCategory;	"representative or reference"
+    uint taxId index;	"www.ncbi.nlm.nih.gov/taxonomy/?term=xxx"
+    uint speciesTaxid;	"www.ncbi.nlm.nih.gov/taxonomy/?term=xxx"
+    string organismName index[100];	"binomial scientific name"
+    string infraspecificName;	"strain/cultivar/ecotype/breed"
+    string isolate;	"source of sample"
+    string versionStatus;	"latest/suppressed/replaced"
+    string assemblyLevel index;	"Contig/Scaffold/Complete Genome/Chromosome"
+    string releaseType;	"Major/Minor/Patch"
+    string genomeRep;	"Full/Partial"
+    string seqRelDate;	"date YYYY-MM-DD sequence released to INSDC"
+    string asmName;	"submitter supplied name"
+    string asmSubmitter;	"institution submitting assembly"
+    string gbrsPairedAsm;	"GenBank<->RefSeq GCA/GCF relationship"
+    string pairedAsmComp;	"identical/different for GCA<->GCF relationship"
+    string ftpPath;	"ftp.ncbi.nlm.nih.gov/genomes/all/GCx/012/345/678/asmId"
+    string excludedFromRefseq;	"noted reason for exclusion from RefSeq"
+    string relationToTypeMaterial;	"note of assembly relation to sample"
+    string asmNotLiveDate;	"date YYYY-MM-DD assembly suppressed/replaced -- historical files only"
+    string assemblyType;	"haploid/diploid/haploid-with-alt-loci/alternate-pseudohaplotype"
+    string taxonGroup index;	"bacteria/viral/archaea/fungi/metagenomes/invertebrate/other/vertebrate_other/plant/vertebrate_mammalian/protozoa"
+    bigint genomeSize;	"total length of all top-level sequences in the primary assembly"
+    bigint genomeSizeUngapped;	"genome length not counting gaps (gap == 10 or more Ns)"
+    float gcPercent;	"GC percent"
+    ushort repliconCount;	"total number of chromosomes, organelle genomes and plasmids"
+    uint scaffoldCount;	"number of scaffolds: placed, unlocalized, unplaced, alternate loci and patch"
+    uint contigCount;	"number of contigs in the primary assembly"
+    string annotationProvider;	"the group that provided the annotation on the assembly"
+    string annotationName;	"the name of the annotation"
+    string annotationDate;	"annotation date YYYY-MM-DD"
+    uint totalGeneCount;	"total gene count in annotation"
+    uint proteinCodingGeneCount;	"protein coding gene count in annotation"
+    uint nonCodingGeneCount;	"non coding gene count in annotation"
+    lstring pubmedId;	"semicolon separated list of PubMed ID(s)"
+    )