18a7959f18910bf26ec02f4ae21b839024d94230
angie
  Wed Feb 8 20:52:35 2023 -0800
Fixed some bash syntax so the usage message appears when needed.

diff --git src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
index ccec350..314cd60 100755
--- src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
+++ src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
@@ -1,182 +1,182 @@
 #!/bin/bash
 set -beEu -x -o pipefail
 
 #	Do not modify this script, modify the source tree copy:
 #	kent/src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
 
 usage() {
     echo "usage: $0 prevDate today problematicSitesVcf [baseProtobuf]"
     echo "This assumes that ncbi.latest and cogUk.latest links/directories have been updated."
 }
 
-if [ $# != 3 && $# != 4 ]; then
+if (( $# != 3 && $# != 4 )); then
   usage
   exit 1
 fi
 
 prevDate=$1
 today=$2
 problematicSitesVcf=$3
 if [ $# == 4 ]; then
     baseProtobuf=$4
 else
     baseProtobuf=
 fi
 
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 cncbDir=$ottoDir/cncb.latest
 gisaidDir=/hive/users/angie/gisaid
 epiToPublic=$gisaidDir/epiToPublicAndDate.latest
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 source $scriptDir/util.sh
 
 mkdir -p $ottoDir/$today
 cd $ottoDir/$today
 
 usherDir=~angie/github/usher
 usher=$usherDir/build/usher-sampled
 matUtils=$usherDir/build/matUtils
 matOptimize=$usherDir/build/matOptimize
 
 if [ ! -s new.masked.vcf.gz ]; then
     $scriptDir/makeNewMaskedVcf.sh $prevDate $today $problematicSitesVcf $baseProtobuf
 fi
 
 if [ ! -s gisaidAndPublic.$today.masked.pb ]; then
     # $scriptDir/usherClusterRun.sh $today
     # Instead of the cluster, use Cheng's blazingly fast new usher-sampled:
     time $usher \
         -T 64 -A -e 5 \
         -i prevRenamed.pb \
         -v new.masked.vcf.gz \
         -o merged.pb \
         --optimization_radius 0 --batch_size_per_process 10 \
         > usher.addNew.log 2>usher-sampled.stderr
     # Branch-specific masking
     time $scriptDir/maskDelta.sh merged.pb merged.deltaMasked.pb
     # Prune samples with too many private mutations and internal branches that are too long.
     $matUtils extract -i merged.deltaMasked.pb \
         --max-parsimony 20 \
         --max-branch-length 60 \
         --max-path-length 175 \
         -O -o merged.deltaMasked.filtered.pb
     # Improved matOptimize from branch
     time $matOptimize \
         -T 80 -r 8 -M 2 -S move_log.filtered \
         -i merged.deltaMasked.filtered.pb \
         -o gisaidAndPublic.$today.masked.preTrim.pb \
         >& matOptimize.filtered.log
 
     # Again prune samples with too many private mutations and internal branches that are too long.
     $matUtils extract -i gisaidAndPublic.$today.masked.preTrim.pb \
         --max-parsimony 20 \
         --max-branch-length 60 \
         --max-path-length 175 \
         -O -o gisaidAndPublic.$today.masked.pb
 fi
 
 # Exclude sequences with a very high number of EPPs from future runs
 grep ^Current usher.addNew.log \
 | awk '$16 >= 10 {print $8;}' \
 | awk -F\| '{ if ($3 == "") { print $1; } else { print $2; } }' \
     > tooManyEpps.ids
 cat tooManyEpps.ids >> ../tooManyEpps.ids
 
 $matUtils extract -i gisaidAndPublic.$today.masked.pb -u samples.$today
 
 $scriptDir/combineMetadata.sh $prevDate $today
 
 # 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 $(wc -l < samples.$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 (completely specified by nextstrain.clade-mutations.tsv)
 time $matUtils annotate -T 50 \
     -l \
     -i gisaidAndPublic.$today.masked.pb \
     -P $ottoDir/$prevDate/cladeToPath \
     -M $scriptDir/nextstrain.clade-mutations.tsv \
     -D details.nextclade \
     -o gisaidAndPublic.$today.masked.nextclade.pb \
     >& annotate.nextclade
 
 # Add pangolin lineage annotations to protobuf.
 time $matUtils annotate -T 50 \
     -i gisaidAndPublic.$today.masked.nextclade.pb \
     -P $ottoDir/$prevDate/lineageToPath \
     -M $scriptDir/pango.clade-mutations.tsv \
     -c $ottoDir/$prevDate/lineageToName \
     -f 0.95 \
     -D details.pango \
     -o gisaidAndPublic.$today.masked.nextclade.pangolin.pb \
     >& annotate.pango
 
 # Replace protobuf with annotated protobuf.
 mv gisaidAndPublic.$today.masked{,.unannotated}.pb
 ln -f gisaidAndPublic.$today.masked.nextclade.pangolin.pb gisaidAndPublic.$today.masked.pb
 
 # Save paths and annotations for use tomorrow.
 $matUtils extract -i gisaidAndPublic.$today.masked.pb -C clade-paths
 tail -n+2 clade-paths \
 | grep -E '^[12]' \
 | cut -f 1,3 > cladeToPath
 tail -n+2 clade-paths \
 | grep -E '^[A-Za-z]' \
 | cut -f 1,3 > lineageToPath
 $matUtils summary -i gisaidAndPublic.$today.masked.pb -C sample-clades
 tail -n+2 sample-clades \
 | tawk '{print $2, $1;}' \
 | sort > cladeToName
 tail -n+2 sample-clades \
 | tawk '{print $3, $1;}' \
 | sort > lineageToName
 
 # Add clade & lineage from tree to metadata.
 zcat gisaidAndPublic.$today.metadata.tsv.gz \
 | tail -n+2 \
 | cut -f 1-9 \
 | sort > tmp1
 tail -n+2 sample-clades \
 | sort > tmp2
 paste <(zcat gisaidAndPublic.$today.metadata.tsv.gz | cut -f 1-9 | head -1) \
       <(echo -e "Nextstrain_clade_usher\tpango_lineage_usher") \
     > gisaidAndPublic.$today.metadata.tsv
 join -t$'\t' tmp1 tmp2 \
     >> gisaidAndPublic.$today.metadata.tsv
 pigz -p 8 -f gisaidAndPublic.$today.metadata.tsv
 rm tmp1 tmp2
 
 # EPI_ISL_ ID to public sequence name mapping, so if users upload EPI_ISL IDs for which we have
 # public names & IDs, we can match them.
 cut -f 1,3 $epiToPublic > epiToPublic.latest
 
 # Update links to latest public+GISAID protobuf and metadata in hgwdev cgi-bin directories
 pigz -p 8 -c samples.$today > samples.$today.gz
 for dir in /usr/local/apache/cgi-bin{-angie,-beta,}/hgPhyloPlaceData/wuhCor1; do
     ln -sf `pwd`/gisaidAndPublic.$today.masked.pb $dir/public.plusGisaid.latest.masked.pb
     ln -sf `pwd`/gisaidAndPublic.$today.metadata.tsv.gz \
         $dir/public.plusGisaid.latest.metadata.tsv.gz
     ln -sf `pwd`/hgPhyloPlace.plusGisaid.description.txt $dir/public.plusGisaid.latest.version.txt
     ln -sf `pwd`/epiToPublic.latest $dir/
     ln -sf `pwd`/samples.$today.gz $dir/public.plusGisaid.names.gz
 done
 
 # Make Taxonium v2 protobuf for display
 usher_to_taxonium --input gisaidAndPublic.$today.masked.pb \
     --metadata gisaidAndPublic.$today.metadata.tsv.gz \
     --genbank ~angie/github/taxonium/taxoniumtools/test_data/hu1.gb \
     --columns genbank_accession,country,date,pangolin_lineage,pango_lineage_usher \
     --clade_types=nextstrain,pango \
     --name_internal_nodes \
     --title "$today tree with sequences from GISAID, INSDC, COG-UK and CNCB" \
     --output gisaidAndPublic.$today.masked.taxonium.jsonl.gz
 
 $scriptDir/extractPublicTree.sh $today $prevDate
 
 set +o pipefail
 grep skipping annotate* | cat