9f9a96ab068a76799311c09a2813b0b28f8e7712
lrnassar
  Mon Jul 13 12:52:41 2026 -0700
Order EVE heatmap amino acid rows by class to match the MaveDB track. refs #37763

Change the heatmap row order from alphabetical to physicochemical-amino-acid-class order
(A V L I M F Y W R H K D E S T N Q G C P), matching the MaveDB Experiments heatmap so the
tracks can be compared row-for-row. Rebuilds eve.bb; updates the makedoc, the AutoSql row
label comment, and the description page.

diff --git src/hg/makeDb/doc/hg38/eve.txt src/hg/makeDb/doc/hg38/eve.txt
index a636bb9329a..cc22efaa13d 100644
--- src/hg/makeDb/doc/hg38/eve.txt
+++ src/hg/makeDb/doc/hg38/eve.txt
@@ -1,44 +1,45 @@
 # [Claude/max] EVE - Evolutionary model of Variant Effect (2025-05-28)
 
 # Data downloaded from https://evemodel.org/download/bulk as EVE_all_data.zip.
 # Reference: Frazer et al. (2021) Nature 599:91-95, PMID 34707284.
 # https://doi.org/10.1038/s41586-021-04043-8
 
 mkdir -p /hive/data/genomes/hg38/bed/eve/input
 cd /hive/data/genomes/hg38/bed/eve/input
 wget https://evemodel.org/download/bulk -O EVE_all_data.zip
 unzip EVE_all_data.zip
 # This extracts, among other things, vcf_files_missense_mutations/ with one VCF per protein.
 
 # Convert VCF files to heatmap bigBed format.
 # Each protein becomes one BED12+ entry. Columns = amino acid positions (at codon
-# genomic coordinates), rows = 20 standard amino acids (A-Y).
+# genomic coordinates), rows = 20 standard amino acids ordered by class (A V L I M F Y W R
+# H K D E S T N Q G C P), matching the MaveDB heatmap track.
 # Multiple codon changes encoding the same amino acid substitution are deduplicated
 # (they carry identical EVE scores). Wildtype cells are left empty.
 # Colors: blue (#2166ac) EVE=0 benign, white (#f7f7f7) EVE=0.5 uncertain,
 #         red (#d6604d) EVE=1 pathogenic.
 
 cd /hive/data/genomes/hg38/bed/eve
 python3 ~/kent/src/hg/makeDb/scripts/eve/vcfToEveHeatmap.py \
     input/vcf_files_missense_mutations/ \
     eve_raw.bed
 
 # Two proteins had VCF coordinates on non-standard assembly scaffolds
 # (G6PT1/O43826 on chrCHR_HG2217_PATCH, MAFIP/Q8WZ33 on chrGL000194.1)
 # and were removed by filtering to chromosomes present in chrom.sizes.
 
 bedSort eve_raw.bed eve_sorted.bed
 
 awk 'NR==FNR{valid[$1]=1; next} $1 in valid {print}' \
     /hive/data/genomes/hg38/chrom.sizes \
     eve_sorted.bed > eve_filtered.bed
 
 bedToBigBed -type=bed12+ -tab \
     -as=~/kent/src/hg/makeDb/scripts/eve/eve_heatmap.as \
     eve_filtered.bed \
     /hive/data/genomes/hg38/chrom.sizes \
     eve.bb
 # Result: 2,949 proteins, 1,717,072 total amino acid positions.
 
 mkdir -p /gbdb/hg38/eve
 ln -s /hive/data/genomes/hg38/bed/eve/eve.bb /gbdb/hg38/eve/eve.bb