4efa4aebadc39cb64a256c3489035b00bd2abdc6 angie Wed Sep 8 12:06:50 2021 -0700 Remove dependency on reference.fa from aligning new sequences; add tree-annotated Nextstrain clade and Pango lineage to metadata. diff --git src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh index 5a8a750..b1fdda1 100755 --- src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh +++ src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh @@ -1,151 +1,156 @@ #!/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 date" echo "This assumes that \$date/gisaidAndPublic.\$date.masked.pb has been generated." } if [ $# != 1 ]; then usage exit 1 fi today=$1 ottoDir=/hive/data/outside/otto/sarscov2phylo cncbDir=$ottoDir/cncb.latest scriptDir=$(dirname "${BASH_SOURCE[0]}") source $scriptDir/util.sh usherDir=~angie/github/usher matUtils=$usherDir/build/matUtils cd $ottoDir/$today # Extract public samples from tree grep -v EPI_ISL_ samples.$today > newPublicNames +# Dunno why, but when I tried using -s together with the filtering params, it ran for 3 hours +# and I killed it -- stuck in a loop? Run two commands: $matUtils extract -i gisaidAndPublic.$today.masked.pb \ -s newPublicNames \ + -o public-$today.all.masked.preTrim.pb +$matUtils extract -i public-$today.all.masked.preTrim.pb \ --max-parsimony 20 \ --max-branch-length 30 \ -O -o public-$today.all.masked.pb # Add nextclade annotations to public protobuf if [ -s cladeToName ]; then # Use combined tree's clade assignments to annotate clades on public tree grep -v EPI_ISL cladeToName > cladeToPublicName time $matUtils annotate -T 50 \ -l \ -i public-$today.all.masked.pb \ -c cladeToPublicName \ -f 0.95 \ -D details.nextclade.public \ -o public-$today.all.masked.nextclade.pb \ >& annotate.nextclade.public else time $matUtils annotate -T 50 \ -l \ -i public-$today.all.masked.pb \ -P ../nextstrain.clade-paths.public.tsv \ -o public-$today.all.masked.nextclade.pb fi # Add pangolin lineage annotations to public protobuf if [ -s lineageToName ]; then grep -v EPI_ISL lineageToName > lineageToPublicName time $matUtils annotate -T 50 \ -i public-$today.all.masked.nextclade.pb \ -c lineageToPublicName \ -f 0.95 \ -D details.pango.public \ -o public-$today.all.masked.nextclade.pangolin.pb \ >& annotate.pango.public else time $matUtils annotate -T 50 \ -i public-$today.all.masked.nextclade.pb \ -P ../pango.clade-paths.public.tsv \ -o public-$today.all.masked.nextclade.pangolin.pb fi # Extract Newick and VCF from public-only tree time $matUtils extract -i public-$today.all.masked.pb \ -t public-$today.all.nwk \ -v public-$today.all.masked.vcf time gzip -f public-$today.all.masked.vcf zcat gisaidAndPublic.$today.metadata.tsv.gz \ | grep -v EPI_ISL_ \ | gzip -c \ > public-$today.metadata.tsv.gz rm public-$today.all.masked.pb ln -f public-$today.all.masked.nextclade.pangolin.pb public-$today.all.masked.pb 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; NCBI and COG-UK sequences downloaded $today; CNCB sequences downloaded $cncbDate" \ > version.txt $matUtils extract -i public-$today.all.masked.pb -u samples.public.$today sampleCountComma=$(echo $(wc -l < samples.public.$today) \ | sed -re 's/([0-9]+)([0-9]{3})$/\1,\2/; s/([0-9]+)([0-9]{3},[0-9]{3})$/\1,\2/;') echo "$sampleCountComma genomes from GenBank, COG-UK and CNCB ($today); sarscov2phylo 13-11-20 tree with newer sequences added by UShER" \ > hgPhyloPlace.description.txt # Make Taxodium-formatted protobuf for display zcat /hive/data/genomes/wuhCor1/goldenPath/bigZips/genes/ncbiGenes.gtf.gz > ncbiGenes.gtf +zcat /hive/data/genomes/wuhCor1/wuhCor1.fa.gz > wuhCor1.fa zcat public-$today.metadata.tsv.gz > metadata.tmp.tsv time $matUtils extract -i public-$today.all.masked.pb \ - -f reference.fa \ + -f wuhCor1.fa \ -g ncbiGenes.gtf \ -M metadata.tmp.tsv \ --write-taxodium public-$today.all.masked.taxodium.pb -rm metadata.tmp.tsv +rm metadata.tmp.tsv wuhCor1.fa gzip public-$today.all.masked.taxodium.pb # Link to public trees download directory hierarchy archiveRoot=/hive/users/angie/publicTrees read y m d < <(echo $today | sed -re 's/-/ /g') archive=$archiveRoot/$y/$m/$d mkdir -p $archive gzip -c public-$today.all.nwk > $archive/public-$today.all.nwk.gz ln -f `pwd`/public-$today.all.masked.{pb,vcf.gz} $archive/ gzip -c public-$today.all.masked.pb > $archive/public-$today.all.masked.pb.gz ln -f `pwd`/public-$today.metadata.tsv.gz $archive/ gzip -c public-$today.all.masked.nextclade.pangolin.pb \ > $archive/public-$today.all.masked.nextclade.pangolin.pb.gz if [ -s lineageToPublicName ]; then gzip -c lineageToPublicName > $archive/lineageToPublicName.tsv.gz else gzip -c ../nextstrain.clade-paths.public.tsv > $archive/nextstrain.clade-paths.public.tsv.gz fi if [ -s cladeToPublicName ]; then gzip -c cladeToPublicName > $archive/cladeToPublicName.tsv.gz else gzip -c ../pango.clade-paths.public.tsv > $archive/pango.clade-paths.public.tsv.gz fi ln -f `pwd`/hgPhyloPlace.description.txt $archive/public-$today.version.txt ln -f `pwd`/public-$today.all.masked.taxodium.pb.gz $archive/ # Update 'latest' in $archiveRoot ln -f $archive/public-$today.all.nwk.gz $archiveRoot/public-latest.all.nwk.gz ln -f $archive/public-$today.all.masked.pb $archiveRoot/public-latest.all.masked.pb ln -f $archive/public-$today.all.masked.pb.gz $archiveRoot/public-latest.all.masked.pb.gz ln -f $archive/public-$today.all.masked.vcf.gz $archiveRoot/public-latest.all.masked.vcf.gz ln -f $archive/public-$today.metadata.tsv.gz $archiveRoot/public-latest.metadata.tsv.gz ln -f $archive/public-$today.version.txt $archiveRoot/public-latest.version.txt ln -f $archive/public-$today.all.masked.taxodium.pb.gz \ $archiveRoot/public-latest.all.masked.taxodium.pb.gz # Update hgdownload-test link for archive mkdir -p /usr/local/apache/htdocs-hgdownload/goldenPath/wuhCor1/UShER_SARS-CoV-2/$y/$m ln -sf $archive /usr/local/apache/htdocs-hgdownload/goldenPath/wuhCor1/UShER_SARS-CoV-2/$y/$m # Update links to latest public protobuf and metadata in hgwdev cgi-bin directories for dir in /usr/local/apache/cgi-bin{-angie,-beta,}/hgPhyloPlaceData/wuhCor1; do ln -sf `pwd`/public-$today.all.masked.pb $dir/public-latest.all.masked.pb ln -sf `pwd`/public-$today.metadata.tsv.gz $dir/public-latest.metadata.tsv.gz ln -sf `pwd`/hgPhyloPlace.description.txt $dir/public-latest.version.txt done