e66bfc81c03088103c395a9a09bda494be3e1132
angie
  Fri Dec 2 11:23:44 2022 -0800
Add more pruning before downsampling: sequences with two or more reversions relative to lineage root, and high mutation density branches.  Add -P file to speed up reannotation on rerooted tree.

diff --git src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
index 23a3144..0e4cdbd 100755
--- src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
+++ src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
@@ -1,119 +1,133 @@
 #!/bin/bash
 source ~/.bashrc
 set -beEu -x -o pipefail
 
 #	Do not modify this script, modify the source tree copy:
 #	kent/src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
 
 usage() {
     echo "usage: $0 buildDate"
 }
 
 if [ $# != 1 ]; then
   usage
   exit 1
 fi
 
 buildDate=$1
 
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 
 usherDir=~angie/github/usher
 matUtils=$usherDir/build/matUtils
 
 today=$(date +%F)
 cd $ottoDir/$buildDate
 
+# Remove sequences that have two or more reversions relative to their assigned clade/lineage.
+$matUtils extract -i gisaidAndPublic.$buildDate.masked.pb --node-stats node-stats
+tawk '$5 > 1 {print $1;}' node-stats > pruneRevs
+$matUtils extract -i gisaidAndPublic.$buildDate.masked.pb \
+    -p -s pruneRevs -O -o gisaidAndPublic.$buildDate.masked.pruneRevs.pb
+
 # Get node ID for root of lineage A, used as reference/root by Pangolin:
-if [ ! -s clade-paths ]; then
-    $matUtils extract -i gisaidAndPublic.$buildDate.masked.pb -C clade-paths
-fi
-lineageARoot=$(grep ^A$'\t' clade-paths | cut -f 2)
+$matUtils extract -i gisaidAndPublic.$buildDate.masked.pruneRevs.pb -C clade-paths.prunedRevs
+lineageARoot=$(grep ^A$'\t' clade-paths.prunedRevs | cut -f 2)
 
-# Reroot protobuf to lineage A:
-$matUtils extract -i gisaidAndPublic.$buildDate.masked.pb \
+# Reroot protobuf to lineage A and restrict to low mutation density (highly supported nodes):
+$matUtils extract -i gisaidAndPublic.$buildDate.masked.pruneRevs.pb \
     --reroot $lineageARoot \
-    -o gisaidAndPublic.$buildDate.masked.reroot.pb
+    --max-mutation-density 2 \
+    -O -o gisaidAndPublic.$buildDate.masked.reroot.pb
 
-# Reroot pango.clade-mutations.tsv; also remove B.1.1.529 (Rachel's request):
+# Reroot pango.clade-mutations.tsv
 grep -w ^A $scriptDir/pango.clade-mutations.tsv \
 | sed -re 's/T28144C( > )?//;  s/C8782T( > )?//;' \
     > pango.clade-mutations.reroot.tsv
 grep -vw ^A $scriptDir/pango.clade-mutations.tsv \
 | sed -re 's/\t/\tT8782C > C28144T > /;' \
-| grep -vF B.1.1.529 \
     >> pango.clade-mutations.reroot.tsv
 
 # Mask additional bases at the beginning and end of the genome that pangolin masks after
 # aligning input sequences.
+set +x
 for ((i=56;  $i <= 265;  i++)); do
     echo -e "N${i}N"
 done > maskPangoEnds
 for ((i=29674;  $i < 29804;  i++)); do
     echo -e "N${i}N"
 done >> maskPangoEnds
+set -x
 $matUtils mask -i gisaidAndPublic.$buildDate.masked.reroot.pb \
     -m maskPangoEnds -o gisaidAndPublic.$buildDate.masked.reroot.pangoMasked.pb
 
+# Preserve lineage annotations that survived rerooting and pango-masking
+$matUtils extract -i gisaidAndPublic.$buildDate.masked.reroot.pangoMasked.pb \
+    -C clade-paths.reroot.pangoMasked
+tail -n+2 clade-paths.reroot.pangoMasked \
+| grep '^[A-Za-z]' \
+| cut -f 1,3 > lineageToPath.reroot.pangoMasked
+
 # Assign updated lineages on the rerooted & pango-masked tree, pango-only for pangolin:
-time $matUtils annotate -T 50 \
+time $matUtils annotate -T 80 \
     -i gisaidAndPublic.$buildDate.masked.reroot.pangoMasked.pb \
+    -P lineageToPath.reroot.pangoMasked \
     -M pango.clade-mutations.reroot.tsv \
     -l \
     -c lineageToName \
     -f 0.95 \
     -u mutations.pangoOnly \
     -D details.pangoOnly \
     -o gisaidAndPublic.$buildDate.masked.reroot.pangoOnly.pb \
     >& annotate.pangoOnly.out
 
 set +o pipefail
 grep 'Could not' annotate.pangoOnly.out | cat
 grep skip annotate.pangoOnly.out | cat
 set -o pipefail
 
 # Make a bunch of smaller trees and see how they do.
 mkdir -p /hive/users/angie/lineageTreeUpdate.$today
 cd /hive/users/angie/lineageTreeUpdate.$today
 for i in 0 1 2 3 4 5 6 7 8 9; do
     echo test.50.$i
     $matUtils extract -i $ottoDir/$buildDate/gisaidAndPublic.$buildDate.masked.reroot.pangoOnly.pb \
         -r 50 -o test.50.$i.pb
     $matUtils mask -i test.50.$i.pb -S -o test.50.$i.simp.pb
 done
 
 # Run pangolin on each subtree
 # 7.5-14.5m each job, ~3.5hrs total:
 conda activate pangolin
 for i in 0 1 2 3 4 5 6 7 8 9; do
     echo test.50.$i.simp
-    time pangolin -t 50 --usher-tree test.50.$i.simp.pb \
-        --skip-designation-hash --no-temp --outdir subset_10000_0.pusher.test.50.$i.simp.out \
+    time pangolin -t 80 --usher-tree test.50.$i.simp.pb \
+        --skip-designation-cache --no-temp --outdir subset_10000_0.pusher.test.50.$i.simp.out \
         ../pangolin_eval/subset_10000_0.fa
 done
 
 # Summarize results
 for i in 0 1 2 3 4 5 6 7 8 9; do
     echo test.50.$i.simp
     tail -n+2 subset_10000_0.pusher.test.50.$i.simp.out/lineage_report.csv \
     | awk -F, '{print $1 "\t" $2;}' \
     | sort \
         > subset_10000_0.pusher.test.50.$i.simp
     join -t$'\t' ../pangolin_eval/subset_10000_0.cogNameToLin subset_10000_0.pusher.test.50.$i.simp \
     | tawk '$2 != $3' \
         > subset_10000_0.pusher.test.50.$i.simp.diff
     cut -f 2,3 subset_10000_0.pusher.test.50.$i.simp.diff \
     | sort | uniq -c | sort -nr > subset_10000_0.pusher.test.50.$i.simp.diffrank
 done
 
 wc -l subset_10000_0.*.diff | sort -n
 
 # Pick the subtree with the fewest differences
 set +o pipefail
 bestTree=$(wc -l subset_10000_0.*.diff | sort -n | head -1 \
            | sed -re 's/.*pusher\.test\.50\.//; s/\.diff//')
 set -o pipefail
 echo $bestTree
 
 # Which lineages have the most differences?
 head subset_10000_0.pusher.test.50.$bestTree.diffrank