5cd81d78c5261be06e848e33cf17c76dfc26ae6b angie Fri Dec 20 15:33:55 2024 -0800 Add nextclade-assigned lineages to metadata; install hgPhyloPlace files in /gbdb instead of cgi-bin. diff --git src/hg/utils/otto/dengue/buildTree.sh src/hg/utils/otto/dengue/buildTree.sh index a3f8362..aba6c7c 100755 --- src/hg/utils/otto/dengue/buildTree.sh +++ src/hg/utils/otto/dengue/buildTree.sh @@ -70,31 +70,31 @@ join -t$'\t' <(sort tweakedMetadata.tsv) accToIdFromTitle.tsv \ | perl -wne 'chomp; @w=split(/\t/); my ($acc, $iso, $loc, $date, $str, $tid) = ($w[0], $w[1], $w[3], $w[4], $w[14], $w[16]); if (! defined $str) { $str = ""; } my $name = $str ? $str : $iso ? $iso : $tid ? $tid : ""; my $country = $loc; $country =~ s/:.*//; my $COU = $country; $COU =~ s/^(\w{3}).*/$1/; $COU = uc($COU); if ($country eq "United Kingdom") { $COU = "UK"; } if ($name !~ /$country/ && $name !~ /\b$COU\b/ && $name ne "") { $name = "$country/$name"; } $name =~ s/[,;]//g; my $year = $date; $year =~ s/-.*//; my $year2 = $year; $year2 =~ s/^\d{2}(\d{2})$/$1/; if ($name ne "" && $name !~ /$year/ && $name !~ /\/$year2$/) { $name = "$name/$year"; } if ($date eq "") { $date = "?"; } my $fullName = $name ? "$name|$acc|$date" : "$acc|$date"; - $fullName =~ s/ /_/g; + $fullName =~ s/[ ,:()]/_/g; print "$acc\t$fullName\n";' \ | sed -re 's/[():'"'"']/_/g; s/\[/_/g; s/\]/_/g;' \ | sed -re 's/_+\|/|/;' \ > renaming.tsv # This builds the whole tree from scratch! Eventually we'll want to add only the new sequences # to yesterday's tree. echo '()' > emptyTree.nwk for subtype in 1 2 3 4; do case $subtype in 1) refFa=$refFa1 gbff=$gbff1 @@ -109,119 +109,130 @@ ;; 3) refFa=$refFa3 gbff=$gbff3 asmAcc=$asmAcc3 archiveRoot=$archiveRoot3 ;; 4) refFa=$refFa4 gbff=$gbff4 asmAcc=$asmAcc4 archiveRoot=$archiveRoot4 ;; esac - # Run nextalign with RefSeq. - nextalign run --input-ref $refFa \ + # Run nextclade -- fortunately they used RefSeqs. + nextclade dataset get --name community/v-gen-lab/dengue/denv$subtype \ + --output-zip denv$subtype.zip + time nextclade run \ + -D denv$subtype.zip \ + -j 32 \ --include-reference \ - --jobs 32 \ + --retry-reverse-complement true \ --output-fasta aligned.$subtype.fa.xz \ + --output-columns-selection seqName,clade,totalSubstitutions,totalDeletions,totalInsertions,totalMissing,totalNonACGTNs,alignmentStart,alignmentEnd,substitutions,deletions,insertions,aaSubstitutions,aaDeletions,aaInsertions,missing,unknownAaRanges,nonACGTNs \ + --output-tsv nextclade.denv$subtype.tsv \ $dengueDir/ncbi/ncbi.$today/genbank.fa.xz \ - >& nextalign.log + >& nextclade.denv$subtype.log # If it becomes necessary, add -excludeFile=$dengueScriptDir/exclude.ids time faToVcf -verbose=2 -includeRef -includeNoAltN \ <(xzcat aligned.$subtype.fa.xz) stdout \ | vcfRenameAndPrune stdin renaming.tsv stdout \ | pigz -p 8 \ > all.$subtype.vcf.gz time $usherSampled -T 64 -A -e 5 \ -t emptyTree.nwk \ -v all.$subtype.vcf.gz \ -o denv$subtype.$today.preFilter.pb\ --optimization_radius 0 --batch_size_per_process 10 \ > usher.addNew.$subtype.log 2>usher-sampled.$subtype.stderr # Filter out branches that are so long they must lead to some other subtype $matUtils extract -i denv$subtype.$today.preFilter.pb \ --max-branch-length 1000 \ -O -o denv$subtype.$today.preOpt.pb >& tmp.log # Optimize: time $matOptimize -T 64 -r 20 -M 2 -S move_log.$subtype \ -i denv$subtype.$today.preOpt.pb \ -o denv$subtype.$today.pb \ >& matOptimize.$subtype.log rm -f *.pbintermediate*.pb chmod 664 denv$subtype.$today.pb # Make metadata that uses same names as tree - echo -e "strain\tgenbank_accession\tdate\tcountry\tlocation\tlength\thost\tbioproject_accession\tbiosample_accession\tsra_accession\tauthors\tpublications" \ + echo -e "strain\tgenbank_accession\tdate\tcountry\tlocation\tlength\thost\tbioproject_accession\tbiosample_accession\tsra_accession\tauthors\tpublications\tNextclade_lineage" \ > denv$subtype.$today.metadata.tsv sort $dengueNcbiDir/metadata.tsv \ | perl -F'/\t/' -walne '$F[3] =~ s/(: ?|$)/\t/; print join("\t", @F);' \ - | join -t$'\t' -o 1.2,2.1,2.6,2.4,2.5,2.8,2.9,2.10,2.11,2.12,2.14,2.15 \ + | join -t$'\t' -o 1.1,1.1,1.6,1.4,1.5,1.8,1.9,1.10,1.11,1.12,1.14,1.15,2.2 \ + - <(cut -f 1,2 nextclade.denv$subtype.tsv | sort) \ + | join -t$'\t' -o 1.2,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9,2.10,2.11,2.12,2.13 \ <(sort renaming.tsv) \ - \ | sort \ >> denv$subtype.$today.metadata.tsv pigz -f -p 8 denv$subtype.$today.metadata.tsv # Make a tree version description for hgPhyloPlace $matUtils extract -i denv$subtype.$today.pb -u samples.$subtype.$today >& tmp.log sampleCountComma=$(wc -l < samples.$subtype.$today \ | sed -re 's/([0-9]+)([0-9]{3})$/\1,\2/; s/([0-9]+)([0-9]{3},[0-9]{3})$/\1,\2/;') echo "$sampleCountComma genomes from INSDC (GenBank/ENA/DDBJ) ($today)" \ > hgPhyloPlace.description.$subtype.txt # Make a taxonium view usher_to_taxonium --input denv$subtype.$today.pb \ --metadata denv$subtype.$today.metadata.tsv.gz \ - --columns genbank_accession,country,location,date,authors \ + --columns genbank_accession,country,location,date,authors,Nextclade_lineage \ --genbank $gbff \ --name_internal_nodes \ --title "Dengue subtype "$subtype" $today tree with $sampleCountComma genomes from INSDC" \ --output denv$subtype.$today.taxonium.jsonl.gz \ >& usher_to_taxonium.$subtype.log - # Update links to latest protobuf and metadata in hgwdev cgi-bin directories -#*** for dir in /usr/local/apache/cgi-bin{-angie,,-beta}/hgPhyloPlaceData/$asmAcc; do - for dir in /usr/local/apache/cgi-bin-angie/hgPhyloPlaceData/$asmAcc; do + # Update links in /gbdb + nc=$(basename $gbff .gbff) + dir=/gbdb/wuhCor1/hgPhyloPlaceData/dengue/$nc + mkdir -p $dir ln -sf $(pwd)/denv$subtype.$today.pb $dir/denv$subtype.latest.pb ln -sf $(pwd)/denv$subtype.$today.metadata.tsv.gz $dir/denv$subtype.latest.metadata.tsv.gz ln -sf $(pwd)/hgPhyloPlace.description.$subtype.txt $dir/denv$subtype.latest.version.txt - done + # Extract Newick and VCF for anyone who wants to download those instead of protobuf $matUtils extract -i denv$subtype.$today.pb \ -t denv$subtype.$today.nwk \ -v denv$subtype.$today.vcf >& tmp.log pigz -p 8 -f denv$subtype.$today.nwk denv$subtype.$today.vcf # Link to public trees download directory hierarchy read y m d < <(echo $today | sed -re 's/-/ /g') archive=$archiveRoot/$y/$m/$d mkdir -p $archive ln -f $(pwd)/denv$subtype.$today.{nwk,vcf,metadata.tsv,taxonium.jsonl}.gz $archive/ gzip -c denv$subtype.$today.pb > $archive/denv$subtype.$today.pb.gz ln -f $(pwd)/hgPhyloPlace.description.$subtype.txt $archive/denv$subtype.$today.version.txt # Update 'latest' in $archiveRoot for f in $archive/denv$subtype.$today.*; do latestF=$(echo $(basename $f) | sed -re 's/'$today'/latest/') ln -f $f $archiveRoot/$latestF done # Update hgdownload-test link for archive asmDir=$(echo $asmAcc \ | sed -re 's@^(GC[AF])_([0-9]{3})([0-9]{3})([0-9]{3})\.([0-9]+)@\1/\2/\3/\4/\1_\2\3\4.\5@') - mkdir -p /usr/local/apache/htdocs-hgdownload/hubs/$asmDir/UShER_DENV-$subtype/$y/$m - ln -sf $archive /usr/local/apache/htdocs-hgdownload/hubs/$asmDir/UShER_DENV-$subtype/$y/$m + mkdir -p /data/apache/htdocs-hgdownload/hubs/$asmDir/UShER_DENV-$subtype/$y/$m + ln -sf $archive /data/apache/htdocs-hgdownload/hubs/$asmDir/UShER_DENV-$subtype/$y/$m # rsync to hgdownload hubs dir - rsync -v -a -L --delete /usr/local/apache/htdocs-hgdownload/hubs/$asmDir/UShER_DENV-$subtype/* \ - qateam@hgdownload.soe.ucsc.edu:/mirrordata/hubs/$asmDir/UShER_DENV-$subtype/ + for h in hgdownload1 hgdownload2; do + rsync -a -L --delete /data/apache/htdocs-hgdownload/hubs/$asmDir/UShER_DENV-$subtype/* \ + qateam@$h:/mirrordata/hubs/$asmDir/UShER_DENV-$subtype/ + done done rm -f mutation-paths.txt *.pre*.pb final-tree.nh nice gzip -f *.log *.tsv move_log* *.stderr samples.*