# [Claude/lrnassar] popEVE - proteome-wide missense deleteriousness scores (2026-06-30)

# popEVE places missense variants on a single proteome-wide, human-specific spectrum of
# deleteriousness by calibrating EVE + ESM-1v evolutionary scores against UK Biobank
# population variation with a Gaussian process.
# Reference: Orenbuch et al. (2025) Nat Genet 57:3165-3174, PMID 41286104.
# https://doi.org/10.1038/s41588-025-02400-1

# Data: the complete UKBB-trained GRCh38 VCF (popEVE v1.1, dated 2025-07-15) from the
# pop.evemodel.org bulk downloads. The VCF carries, per missense substitution, genomic
# coordinates plus INFO fields protein (RefSeq NP_), gene, mutant (e.g. E773D),
# gap_frequency, popEVE, pop-adjusted_EVE, pop-adjusted_ESM1v, EVE, ESM1v.
# Source size 1476124568 bytes, Last-Modified 2025-10-29.

mkdir -p /hive/data/outside/popEve
mkdir -p /hive/data/genomes/hg38/bed/popEve/sorttmp
cd /hive/data/genomes/hg38/bed/popEve
ln -s /hive/data/outside/popEve input

cd /hive/data/outside/popEve
wget -nv https://data.evemodel.org/popeve/v1.1/downloads/grch38_popEVE_ukbb_20250715.vcf.gz

# NOTE: the steps in this section produce the intermediate SPARSE heatmap. The final track is
# DENSE (all 19 substitutions per position); see the DENSE REBUILD section below. These steps
# still run because they produce popEve_sorted.tsv, the codon-coordinate and strand source
# reused by the dense build.
#
# The combined VCF is one position-sorted file with all proteins interleaved (overlapping
# genes share positions), so records are grouped by protein on disk before conversion.
# Each protein becomes one heatmap BED12+ entry: columns = amino acid positions at codon
# 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 carry identical popEVE scores and are deduplicated.
# Wildtype cells are empty. popEVE lists only positions carrying a missense alt, so a codon
# may have only 2 of its 3 genomic positions; block sizes are clamped (min(3, gap-to-next))
# so adjacent codon blocks cannot overlap, which keeps the file valid for bedToBigBed.
# Strand is taken from NCBI RefSeq (the VCF has no strand field), cross-checked against the
# strand inferred from genomic-vs-protein-position direction.
# Color: global cross-gene gradient keyed to raw popEVE; interior anchors at the published
# severe (-5.056) and moderate (-4.617) cutoffs and the proteome median (~-3.5); outer
# saturation anchors at the 0.5th / 99.5th percentiles of the proteome-wide distribution.
# Records with popEVE=nan (e.g. start-codon M1 variants) are skipped.

cd /hive/data/genomes/hg38/bed/popEve
# Full build (download already done): strand map, extract, color anchors, sort, convert,
# filter to chrom.sizes, bigBed. See runBuild.sh in this directory.
bash runBuild.sh

# runBuild.sh steps, in order:
#   1. NP_->strand map:
#        hgsql hg38 -N -e "select distinct l.protAcc, g.chrom, g.strand from ncbiRefSeqLink l
#          join ncbiRefSeq g on g.name=l.mrnaAcc where l.protAcc like 'NP\_%'"
#        -> np_strand.tsv (prefer the strand on a primary chromosome)
#   2. extract: zcat ...vcf.gz | extractPopEve.py > popEve_records.tsv
#   3. color anchors: p0.5 / p99.5 of popEVE over all records -> anchors.txt
#   4. sort -t$'\t' -k1,1 -k4,4n -S 4G -T sorttmp popEve_records.tsv > popEve_sorted.tsv
#   5. vcfToPopEveHeatmap.py popEve_sorted.tsv np_strand.tsv popEve_raw.bed $LO $HI
#   6. bedSort + awk filter to chrom.sizes -> popEve_filtered.bed
#   7. bedToBigBed -type=bed12+ -tab -as=popEve_heatmap.as popEve_filtered.bed chrom.sizes popEve_sparse.bb
#      (distinct name from the dense popEve.bb so re-running this sparse build cannot clobber it)
# Scripts (all in ~/kent/src/hg/makeDb/scripts/popEve/): extractPopEve.py,
#   vcfToPopEveHeatmap.py, popEve_heatmap.as, and the build drivers runBuild.sh (sparse /
#   coordinate foundation) and runBuildDense.sh (dense rebuild).

# Notes:
#  - The genomic VCF contains only single-nucleotide-reachable substitutions (~6-9 of 19 per
#    codon). The DENSE REBUILD below supersedes this with the full per-amino-acid matrix; the
#    VCF-derived popEve_sorted.tsv remains the source of genomic codon coordinates and strand.
#  - The heatmap renderer parses the score array (chopCommas, keeps trailing empty) and the
#    label array (chopByCharRespectDoubleQuotesKeepEmpty, drops one trailing empty)
#    differently. When the last cell (last row, last column) is empty the counts disagree and
#    the track aborts; the converter sets a non-empty placeholder label on that one trailing
#    cell (its score stays empty so the cell is uncolored). trailingFix count below.

# Build results:
#   records extracted: 66,400,085 (nan skipped: 15,156)
#   color anchors: loAnchor=-5.742 hiAnchor=-2.287 (popEVE p0.5 / p99.5; median -3.358)
#   proteins: 18,968 (18,343 distinct gene symbols; remainder are RefSeq isoforms)
#   amino-acid positions: 10,114,809;  bases covered: 886,638,890
#   strand: 0 inferred-vs-RefSeq mismatches; 25 proteins not in the RefSeq map (strand from
#     coordinate inference); 0 with no strand signal; 0 dropped by chrom.sizes filter
#   trailingFix (trailing empty cell relabeled): 15,555 proteins
#   mouseover: HTML multi-line labels (<br>/<b>); component scores rounded to 3 dp;
#     missing/nan components shown as NA
#   popEve_sparse.bb size: 1,592,586,266 bytes

# ============================================================================
# DENSE REBUILD (2026-07-23) - full per-amino-acid matrix, per collaborator request
# ============================================================================
# The popEVE authors confirmed the per-transcript CSV download carries the COMPLETE
# per-amino-acid matrix (all 19 substitutions per position), unlike the genomic VCF above
# (single-nucleotide-reachable only, ~6 of 19 per codon). This rebuild takes the SCORES from
# the per-transcript CSVs and REUSES the genomic codon coordinates, strand, and blocks
# already derived from the VCF (popEve_sorted.tsv), producing dense heatmaps. Proteins present
# in the VCF but absent from the (older, March 2025) CSV release fall back to sparse VCF scores.

cd /hive/data/outside/popEve
wget -nv https://data.evemodel.org/popeve/v1.1/downloads/popEVE_ukbb_20250312.zip
#   2915714283 bytes, Last-Modified 2025-10-29
mkdir -p popeve_csv
unzip -q popEVE_ukbb_20250312.zip -d popeve_csv/
#   18,332 per-transcript CSVs at popeve_csv/popEVE_ukbb_20250312/<NP_acc>.csv
#   columns: mutant,gap frequency,popEVE,popped EVE,popped ESM-1v,EVE,ESM-1v

cd /hive/data/genomes/hg38/bed/popEve
bash runBuildDense.sh
# runBuildDense.sh steps:
#   1. proteins not in the CSV (sparse fallback): 637
#   2. color anchors: p0.5 / p99.5 of popEVE over the full matrix (all CSV popEVE values plus
#      VCF popEVE for the 637 non-CSV proteins) -> anchorsDense.txt
#   3. vcfToPopEveHeatmap.py popEve_sorted.tsv np_strand.tsv popEve_dense_raw.bed $LO $HI <csvDir>
#        the optional <csvDir> arg enables dense mode; loadCsv() fills all 19 substitutions
#        per position from the CSV, keeping the VCF codon coordinates and wildtype residue
#   4. bedSort + filter to chrom.sizes + bedToBigBed -> popEve.bb

# Dense build results:
#   full-matrix popEVE values: 187,547,662
#   color anchors: loAnchor=-6.035 hiAnchor=-2.407 (popEVE p0.5 / p99.5; median -3.489)
#   proteins: 18,968 (dense 18,331 from CSV; sparse 637 VCF fallback)
#   NP_065910.3 (SHROOM3) is in the CSV but not the VCF coordinate set (all its VCF records
#     were nan-skipped start codons), so its dense matrix is unused -> 18,331 dense, not 18,332
#   wtMismatch 0 (CSV and VCF wildtype residues agree); posSparse 0 (every dense position
#     also had CSV coverage); trailingFix 1043. The converter skips CSV rows with a nan/empty
#     popEVE and skips positions where the CSV wildtype disagrees with the genomic one; both
#     are 0 in this build (empty-popEVE rows already render as empty cells).
#   popEve.bb size: 4,726,263,622 bytes

mkdir -p /gbdb/hg38/popEve
ln -sf /hive/data/genomes/hg38/bed/popEve/popEve.bb /gbdb/hg38/popEve/popEve.bb
