d091ea9bacb0841f1aa4b17b5f1e8a5219b43929
angie
  Sat Apr 22 18:25:31 2023 -0700
Get new sequences from CNCB.

diff --git src/hg/utils/otto/sarscov2phylo/updatePublic.sh src/hg/utils/otto/sarscov2phylo/updatePublic.sh
index e74c4e7..bd3c79c 100755
--- src/hg/utils/otto/sarscov2phylo/updatePublic.sh
+++ src/hg/utils/otto/sarscov2phylo/updatePublic.sh
@@ -1,78 +1,82 @@
 #!/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/updatePublic.sh
 
 usage() {
     echo "usage: $0 problematicSitesVcf"
 }
 
 if [ $# != 1 ]; then
   usage
   exit 1
 fi
 
 problematicSitesVcf=$1
 
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 gisaidDir=/hive/users/angie/gisaid
 
 today=$(date +%F)
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 
 $scriptDir/gisaidFromChunks.sh &
 
 cogUkDir=$ottoDir/cogUk.$today
 mkdir -p $cogUkDir
 cd $cogUkDir && time $scriptDir/getCogUk.sh >& getCogUk.log &
 
 ncbiDir=$ottoDir/ncbi.$today
 mkdir -p $ncbiDir
 cd $ncbiDir && time $scriptDir/getNcbi.sh >& getNcbi.log &
 
+cncbDir=$ottoDir/cncb.$today
+mkdir -p $cncbDir
+cd $cncbDir && time $scriptDir/getCncb.sh >& getCncb.log &
+
 wait
 
 time $scriptDir/updateIdMapping.sh \
     $gisaidDir/{metadata_batch_$today.tsv.gz,sequences_batch_$today.fa.xz}
 
 buildDir=$ottoDir/$today
 mkdir -p $buildDir
 cd $buildDir
 
 prevDate=$(date -d yesterday +%F)
 time $scriptDir/updateCombinedTree.sh $prevDate $today $problematicSitesVcf \
     >& updateCombinedTree.log
 
 echo ""
 cat hgPhyloPlace.description.txt
 cat hgPhyloPlace.plusGisaid.description.txt
 
 set +o pipefail
 grep skip annotate.pango annotate.nextclade | cat
 grep 'Could not' annotate.pango annotate.nextclade | cat
 
-# Check for newly lineages that are missing from pango.clade-mutations.tsv
+# Check for newly added lineages that are missing from pango.clade-mutations.tsv
 set +x
 lineages=~angie/github/pango-designation/lineages.csv
 tail -n+2 $lineages | cut -d, -f 2 | uniq | grep -E '^(AY|[B-Z][A-Z])' | sort -u \
     > $TMPDIR/designatedDoubleLetters
 cut -f 1 $scriptDir/pango.clade-mutations.tsv  \
 | grep -E '^(AY|[B-Z][A-Z])' | grep -v _ | sort -u \
     > $TMPDIR/cladeMutDoubleLetters
 missingLineages=$(comm -23 $TMPDIR/designatedDoubleLetters $TMPDIR/cladeMutDoubleLetters)
 if [[ "$missingLineages" != "" ]]; then
     echo "LINEAGES MISSING FROM lineages.csv:"
     echo $missingLineages
 fi
 extraLineages=$(comm -13 $TMPDIR/designatedDoubleLetters $TMPDIR/cladeMutDoubleLetters)
 if [[ "$extraLineages" != "" ]]; then
     echo "EXTRA LINEAGES (withdrawn?) in pango.clade-mutations.tsv:"
     echo $extraLineages
 fi
 set -o pipefail
 set -x
 
 # Clean up
 nice xz -f new*fa &