b46cc2178f40ac4831d5896d96523677c04f36d9
angie
  Tue Apr 13 23:15:41 2021 -0700
More accurate sample count for combined tree.

diff --git src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
index 5a8eb09..ccc5640 100755
--- src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
+++ src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
@@ -184,31 +184,32 @@
 mv uncondensed-final-tree.nh gisaidAndPublic.$today.nwk
 
 # Metadata for hgPhyloPlace: for now, start with already-built public metadata.
 zcat public-$today.metadata.tsv.gz > gisaidAndPublic.$today.metadata.tsv
 zcat $gisaidDir/metadata_batch_$today.tsv.gz \
 | grep -Fwf <(cut -f 2 $renaming | grep EPI_ISL | cut -d\| -f 2) \
 | tawk '{print $1 "|" $3 "|" $5, "", $5, $7, $15, $13, $14, $18, $19;}' \
     >> gisaidAndPublic.$today.metadata.tsv
 wc -l gisaidAndPublic.$today.metadata.tsv
 gzip gisaidAndPublic.$today.metadata.tsv
 
 # version/description files
 cncbDate=$(ls -l $cncbDir | sed -re 's/.*cncb\.([0-9]{4}-[0-9][0-9]-[0-9][0-9]).*/\1/')
 echo "sarscov2phylo release 13-11-20; GISAID, NCBI and COG-UK sequences downloaded $today; CNCB sequences downloaded $cncbDate" \
     > version.plusGisaid.txt
-sampleCountComma=$(echo $(wc -l < $renaming) \
+$matUtils extract -i gisaidAndPublic.$today.masked.pb -u samples.$today
+sampleCountComma=$(echo $(wc -l < samples.$today) \
                    | sed -re 's/([0-9]+)([0-9]{3})$/\1,\2/; s/([0-9]+)([0-9]{3},[0-9]{3})$/\1,\2/;')
 echo "$sampleCountComma genomes from GISAID, GenBank, COG-UK and CNCB ($today); sarscov2phylo 13-11-20 tree with newer sequences added by UShER" \
     > hgPhyloPlace.plusGisaid.description.txt
 
 # Add nextclade annotations to protobuf
 zcat gisaidAndPublic.$today.metadata.tsv.gz \
 | tail -n+2 | tawk '$8 != "" {print $8, $1;}' \
 | sed -re 's/^20E \(EU1\)/20E.EU1/;' \
     > cladeToName
 time $matUtils annotate -T 50 \
     -l \
     -i gisaidAndPublic.$today.masked.pb \
     -c cladeToName \
     -o gisaidAndPublic.$today.masked.nextclade.pb \
     >& annotate.nextclade.out