01859939a397ed998e752ad25c54cdd22742a49c
angie
  Fri Dec 20 15:00:05 2024 -0800
Lots of additions for H5N1 outbreak work.
* Add Andersen Lab's assemblies of USDA SRA data from 2024 H5N1 outbreak
* Add Bloom Lab metadata from Deep Mutational Scanning (DMS) experiments on H5N1 HA (referenced to American Wigeon 2021 vaccine strain) and PB2
* Add build of concatenated segments from the 2024 H5N1 outbreak
* Better handling of serotype and segment in INSDC metadata

diff --git src/hg/utils/otto/fluA/buildConcatTree.sh src/hg/utils/otto/fluA/buildConcatTree.sh
new file mode 100755
index 0000000..68f1fca
--- /dev/null
+++ src/hg/utils/otto/fluA/buildConcatTree.sh
@@ -0,0 +1,302 @@
+#!/bin/bash
+source ~/.bashrc
+set -beEu -o pipefail
+
+# Concatenate the segments of sequences in the 2024 H5N1 outbreak and build a tree & metadata.
+
+today=$1
+if [[ $today == "" ]]; then
+    today=$(date +%F)
+fi
+
+fluADir=/hive/data/outside/otto/fluA
+fluANcbiDir=$fluADir/ncbi/ncbi.latest
+fluAScriptDir=$(dirname "${BASH_SOURCE[0]}")
+
+archiveRoot=/hive/users/angie/publicTreesFluA
+downloadsRoot=/data/apache/htdocs-hgdownload/hubs
+
+assemblyDir=/hive/data/outside/ncbi/genomes
+asmAcc=GCF_000864105.1
+asmDir=$(echo $asmAcc \
+         | sed -re 's@^(GC[AF])_([0-9]{3})([0-9]{3})([0-9]{3})\.([0-9]+)@\1/\2/\3/\4/\1_\2\3\4.\5@')
+assemblyReport=$assemblyDir/$asmDir*/$asmAcc*_assembly_report.txt
+
+threads=32
+
+
+# Assembly reports have segment numbers but not names, so map like this:
+function segName {
+    case $1 in
+        1)
+            echo PB2
+            ;;
+        2)
+            echo PB1
+            ;;
+        3)
+            echo PA
+            ;;
+        4)
+            echo HA
+            ;;
+        5)
+            echo NP
+            ;;
+        6)
+            echo NA
+            ;;
+        7)
+            echo MP
+            ;;
+        8)
+            echo NS
+            ;;
+        *)
+            echo ERROR
+            ;;
+    esac
+}
+
+# INSDC accession of basal sequence for each segment
+function segRefAcc {
+    case $1 in
+        1)
+            echo PP755620.1
+            ;;
+        2)
+            echo PP755619.1
+            ;;
+        3)
+            echo PP755618.1
+            ;;
+        4)
+            echo PP753693.1
+            ;;
+        5)
+            echo PP755616.1
+            ;;
+        6)
+            echo PP753695.1
+            ;;
+        7)
+            echo PP755614.1
+            ;;
+        8)
+            echo PP753097.1
+            ;;
+        *)
+            echo ERROR
+            ;;
+    esac
+}
+
+
+cd $fluADir/build/$today
+
+# First, for each segment, find the node of the segment tree that corresponds to the outbreak.
+
+# A/cattle/Texas/24-008749-007/2024 is basal for segments 1 (PB2), 2 (PB1), 3 (PA), 5 (NP) and 7 (M)
+for seg in 1 2 3 5 7; do
+    segRef=$(grep NC_ $assemblyReport | tawk '$3 == '$seg' {print $7;}')
+    $matUtils extract -i fluA.$asmAcc.$segRef.$today.pb -S sample-paths.$asmAcc.$segRef \
+        >& tmp.log
+    cladeNode=$(grep Texas/24-008749-007/2024 sample-paths.$asmAcc.$segRef \
+        | awk '{print $NF;}' \
+        | sed -re 's/:.*//;')
+    grep -w $cladeNode sample-paths.$asmAcc.$segRef \
+    | cut -f 1 > samples.h5n1_outbreak_2024.$seg
+done
+
+# A/cattle/New_Mexico/24-010193-003/2024 is basal for segments 4 (HA) and 6 (NA)
+for seg in 4 6; do
+    segRef=$(grep NC_ $assemblyReport | tawk '$3 == '$seg' {print $7;}')
+    $matUtils extract -i fluA.$asmAcc.$segRef.$today.pb -S sample-paths.$asmAcc.$segRef \
+        >& tmp.log
+    cladeNode=$(grep New_Mexico/24-010193-003/2024 sample-paths.$asmAcc.$segRef \
+        | awk '{print $NF;}' \
+        | sed -re 's/:.*//;')
+    grep -w $cladeNode sample-paths.$asmAcc.$segRef \
+    | cut -f 1 > samples.h5n1_outbreak_2024.$seg
+done
+
+# A/cattle/Texas/24-009110-018/2024 is basal for segment 8 (NS) - but it's not in the H5N1
+# NS tree (reassortment since original H5N1 NS, too distant to align)
+asmAcc=GCF_000851145.1
+seg=8
+segRef=NC_004906.1
+$matUtils extract -i fluA.$asmAcc.$segRef.$today.pb -S sample-paths.$asmAcc.$segRef \
+        >& tmp.log
+cladeNode=$(grep Texas/24-009110-018/2024 sample-paths.$asmAcc.$segRef \
+    | awk '{print $NF;}' \
+    | sed -re 's/:.*//;')
+grep -w $cladeNode sample-paths.$asmAcc.$segRef \
+| cut -f 1 > samples.h5n1_outbreak_2024.$seg
+
+# Use GenBank sequences found in the trees plus all Andersen Lab assembled sequences.
+# Exclude some sequences that would require the root to be further back than my selected segments.
+cat samples.h5n1_outbreak_2024.* | grep -v \|SRR | cut -d\| -f 2 \
+| grep -Fwf - $fluANcbiDir/metadata.tsv \
+| cut -f 15 | sort -u \
+| grep -vE 'A/Texas/37/2024|24-003692-001|24-005915-001|23-038138-001|24-006483-001' \
+| grep -Ff - $fluANcbiDir/metadata.tsv \
+| cut -f 1,17 \
+    > cladeAccToSeg
+# Extract the sequences into per-segment fasta files... renamed from accession to tree name.
+# joinSegments.py below will ignore the uniquifying INSDC accession part of names.  Remove the
+# uniquifying segment name from Andersen Lab sequences.
+for seg in 1 2 3 4 5 6 7 8; do
+    tawk '$2 == '$seg' {print $1;}' cladeAccToSeg \
+    | faSomeRecords <(xzcat $fluANcbiDir/genbank.fa.xz) stdin stdout \
+    | faRenameRecords stdin renaming.tsv.gz h5n1_outbreak_2024.$seg.fa
+    segName=$(segName $seg)
+    fastaNames $fluADir/andersen_lab.srrNotGb.renamed.fa | grep _$segName/ \
+    | faSomeRecords $fluADir/andersen_lab.srrNotGb.renamed.fa stdin stdout \
+    | sed -re '/^>/ s@_'$segName'/@/@;' \
+        >> h5n1_outbreak_2024.$seg.fa
+    refAcc=$(segRefAcc $seg)
+    nextclade run --input-ref $fluADir/h5n1_outbreak_2024/$refAcc.fa h5n1_outbreak_2024.$seg.fa \
+    --excess-bandwidth 9 --terminal-bandwidth 100 --allowed-mismatches 4 \
+    --gap-alignment-side right --min-seed-cover 0.1 \
+    --output-fasta h5n1_outbreak_2024.$seg.aligned.fa \
+        >& nextclade.$seg.log
+done
+
+$fluAScriptDir/joinSegments.py \
+    --segments h5n1_outbreak_2024.{1,2,3,4,5,6,7,8}.aligned.fa \
+    --output h5n1_outbreak_2024.aligned.fa \
+    >& joinSegments.log
+
+cat $fluADir/h5n1_outbreak_2024/concat.fa h5n1_outbreak_2024.aligned.fa \
+| faToVcf -verbose=2 -includeNoAltN stdin stdout \
+| pigz -p 8 \
+    > h5n1_outbreak_2024.in.vcf.gz
+
+$usher-sampled -T $threads -A -e 10 \
+    -t emptyTree.nwk \
+    -v h5n1_outbreak_2024.in.vcf.gz \
+    -o h5n1_outbreak_2024.preOpt.pb.gz \
+    --optimization_radius 0 --batch_size_per_process 100 \
+    > usher.addNew.h5n1_outbreak_2024.log 2> usher-sampled.h5n1_outbreak_2024.stderr
+
+# Optimize:
+$matOptimize -T $threads -m 0.00000001 -M 1 -S move_log.h5n1_outbreak_2024 \
+    -i h5n1_outbreak_2024.preOpt.pb.gz \
+    -o h5n1_outbreak_2024.pb.opt.gz \
+    >& matOptimize.h5n1_outbreak_2024.log
+chmod 664 h5n1_outbreak_2024.pb*
+
+# Collapse nodes
+$matUtils extract -i h5n1_outbreak_2024.pb.opt.gz \
+    -O -o h5n1_outbreak_2024.pb.gz
+
+# Make a tree version description for hgPhyloPlace
+$matUtils extract -i h5n1_outbreak_2024.pb.gz -u samples.h5n1_outbreak_2024 \
+    >& tmp.log
+awk -F\| '{if ($3 == "") { print $1; } else { print $2; }}' samples.h5n1_outbreak_2024 \
+    > accs.h5n1_outbreak_2024.tsv
+sampleCountComma=$(wc -l < samples.h5n1_outbreak_2024 \
+    | sed -re 's/([0-9]+)([0-9]{3})$/\1,\2/; s/([0-9]+)([0-9]{3},[0-9]{3})$/\1,\2/;')
+echo "$sampleCountComma genomes from INSDC (GenBank/ENA/DDBJ) or SRA ($today)" \
+    > hgPhyloPlace.description.h5n1_outbreak_2024.txt
+
+# Metadata (no need to add clade because the outbreak is all B3.13)
+echo -e "strain\tdate\tcountry\tlocation\thost\tbioproject_accession\tbiosample_accession\tsra_accession\tauthors\tpublications" \
+    > h5n1_outbreak_2024.metadata.tsv
+# INSDC metadata (from HA segment; remove uniquifying INSDC accessions)
+grep -Fwf <(cut -d\| -f 2 samples.h5n1_outbreak_2024.4 | grep -v ^SRR) $fluANcbiDir/metadata.tsv \
+| sort \
+| perl -F'/\t/' -walne '$F[3] =~ s/(: ?|$)/\t/;  print join("\t", @F);' \
+| join -t$'\t' -o 1.2,2.6,2.4,2.5,2.9,2.10,2.11,2.12,2.14,2.15 \
+    <(zcat renaming.tsv.gz | cut -d\| -f 1,3| sort) \
+    - \
+| sort -u \
+    >> h5n1_outbreak_2024.metadata.tsv
+# Add Andersen lab metadata (from HA segment but remove _HA from names)
+grep _HA/ $fluADir/andersen_lab.srrNotGb.renamed.metadata.tsv \
+| cut -f 1,3-5,7- \
+| sed -re 's@_HA/@/@;' \
+    >> h5n1_outbreak_2024.metadata.tsv
+wc -l h5n1_outbreak_2024.metadata.tsv
+
+# Add Bloom lab's Deep Mutational Scanning scores for HA and PB2
+tail -n+2 h5n1_outbreak_2024.metadata.tsv \
+| sort \
+| join -t$'\t' -a 1 \
+    -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9,2.10,2.11 \
+    - \
+    <(zcat H5N1_HA_DMS_metadata.tsv.gz | tail -n+2 \
+      | sed -re 's/\|[A-Z]{2}[0-9]{6}\.[0-9]+\|/|/; s@_HA/@/@;' | sort -u) \
+| join -t$'\t' -a 1 \
+    -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,1.11,1.12,1.13,1.14,1.15,1.16,1.17,1.18,1.19,1.20,2.2,2.3 \
+    - \
+    <(zcat PB2_DMS_metadata.tsv.gz | tail -n+2 \
+      | sed -re 's/\|[A-Z]{2}[0-9]{6}\.[0-9]+\|/|/; s@_PB2/@/@;' | sort -u) \
+    > tmp
+oldFields=$(head -1 h5n1_outbreak_2024.metadata.tsv | sed -re 's/\t/\\t/g')
+set +o pipefail
+haFields=$(zcat H5N1_HA_DMS_metadata.tsv.gz | cut -f 2- | head -1 | sed -re 's/\t/\\t/g')
+pb2Fields=$(zcat PB2_DMS_metadata.tsv.gz | cut -f 2-3 | head -1 | sed -re 's/\t/\\t/g')
+set -o pipefail
+echo -e "$oldFields\t$haFields\t$pb2Fields" > h5n1_outbreak_2024.metadata.tsv
+cat tmp >> h5n1_outbreak_2024.metadata.tsv
+rm tmp
+pigz -f -p 8 h5n1_outbreak_2024.metadata.tsv
+
+usher_to_taxonium --input h5n1_outbreak_2024.pb.gz \
+    --metadata h5n1_outbreak_2024.metadata.tsv.gz \
+    --columns host,country,location,date,authors,mouse_escape,ferret_escape,cell_entry,stability,sa26_increase,mouse_escape_mutations,ferret_escape_mutations,cell_entry_mutations,stability_mutations,sa26_increase_mutations,mutdiffsel,mutdiffsel_mutations \
+    --genbank $fluADir/h5n1_outbreak_2024/concat.gbff \
+    --name_internal_nodes \
+    --title "2024 H5N1 outbreak in USA, concatenated segments from INSDC and SRA ($today)" \
+    --config_json $fluAScriptDir/concat.config.json \
+    --chronumental \
+    --chronumental_steps 500 \
+    --chronumental_add_inferred_date chronumental_date \
+    --output h5n1_outbreak_2024.jsonl.gz \
+    >& utt.log
+
+# Link to /gbdb/ location
+dir=/gbdb/wuhCor1/hgPhyloPlaceData/influenzaA/h5n1_outbreak_2024
+mkdir -p $dir
+ln -sf $(pwd)/h5n1_outbreak_2024.pb.gz $dir/h5n1_outbreak_2024.latest.pb.gz
+ln -sf $(pwd)/h5n1_outbreak_2024.metadata.tsv.gz $dir/h5n1_outbreak_2024.latest.metadata.tsv.gz
+ln -sf $(pwd)/hgPhyloPlace.description.h5n1_outbreak_2024.txt \
+    $dir/h5n1_outbreak_2024.latest.version.txt
+
+# Extract Newick and VCF for anyone who wants to download those instead of protobuf
+$matUtils extract -i h5n1_outbreak_2024.pb.gz \
+    -t h5n1_outbreak_2024.nwk \
+    -v h5n1_outbreak_2024.vcf >& tmp.log
+pigz -p 8 -f h5n1_outbreak_2024.nwk h5n1_outbreak_2024.vcf
+
+# Make a ref + all fasta download file for Delphy folks
+cat $fluADir/h5n1_outbreak_2024/concat.fa h5n1_outbreak_2024.aligned.fa \
+| pigz -p 8 \
+    > h5n1_outbreak_2024.msa.fa.gz
+
+# Link to public trees archive directory (no assembly/segRef hierarchy, just by date)
+read y m d < <(echo $today | sed -re 's/-/ /g')
+archive=$archiveRoot/$y/$m/$d
+mkdir -p $archive
+ln -f $(pwd)/h5n1_outbreak_2024.{nwk,vcf,pb,metadata.tsv,msa.fa}.gz $archive/
+if [ -s h5n1_outbreak_2024.jsonl.gz ]; then
+    ln -f $(pwd)/h5n1_outbreak_2024.jsonl.gz $archive/
+fi
+ln -f $(pwd)/hgPhyloPlace.description.h5n1_outbreak_2024.txt \
+    $archive/h5n1_outbreak_2024.version.txt
+
+# Update 'latest' in $archiveRoot
+for e in jsonl.gz metadata.tsv.gz nwk.gz pb.gz vcf.gz version.txt msa.fa.gz ; do
+    ln -f $archive/h5n1_outbreak_2024.$e $archiveRoot/h5n1_outbreak_2024.latest.$e
+done
+
+# Update hgdownload-test link for archive (adding assembly/segRef hierarchy)
+mkdir -p $downloadsRoot/$asmDir/UShER_h5n1_outbreak_2024/$y/$m/$d
+ln -sf $archive/h5n1_outbreak_2024.* $downloadsRoot/$asmDir/UShER_h5n1_outbreak_2024/$y/$m/$d/
+ln -sf $archiveRoot/h5n1_outbreak_2024.latest.* $downloadsRoot/$asmDir/UShER_h5n1_outbreak_2024/
+# rsync to hgdownload hubs dir
+for h in hgdownload1 hgdownload2; do
+    rsync -a -L --delete $downloadsRoot/$asmDir/UShER_h5n1_outbreak_2024 \
+        qateam@$h:/mirrordata/hubs/$asmDir/
+done