9734d13d2c7ee8004001a7553145e65af763796a
angie
  Tue Feb 22 11:06:40 2022 -0800
Extract Nextstrain clade from full nextclade output now generated by getNcbi.sh and getCogUk.sh.

diff --git src/hg/utils/otto/sarscov2phylo/combineMetadata.sh src/hg/utils/otto/sarscov2phylo/combineMetadata.sh
index 87265c3..56f5862 100755
--- src/hg/utils/otto/sarscov2phylo/combineMetadata.sh
+++ src/hg/utils/otto/sarscov2phylo/combineMetadata.sh
@@ -56,59 +56,59 @@
     echo Getting GenBank Pangolin lineages from $ncbiDir/lineage_report.csv
     tail -n+2  $ncbiDir/lineage_report.csv \
     | sed -re 's/^([A-Z][A-Z][0-9]{6}\.[0-9]+)[^,]*/\1/;' \
     | awk -F, '$2 != "" && $2 != "None" {print $1 "\t" $2;}' \
     | sort -u \
         > gbToLineage
 else
     echo Getting GenBank Pangolin lineages from $prevMeta
     zcat $prevMeta \
     | tail -n+2 \
     | tawk '$2 != "" && $8 != "" { print $2, $8; }' \
     | sort -u \
         > gbToLineage
 fi
 wc -l gbToLineage
-if [ -e $ncbiDir/nextclade.tsv ]; then
-    sort -u $ncbiDir/nextclade.tsv > gbToNextclade
+if [ -e $ncbiDir/nextclade.full.tsv.gz ]; then
+    zcat $ncbiDir/nextclade.full.tsv.gz | cut -f 1,2 | sed -re 's/"//g;' | sort -u > gbToNextclade
 else
     touch gbToNextclade
 fi
 wc -l gbToNextclade
 join -t$'\t' -a 1 gb.metadata gbToNextclade \
 | join -t$'\t' -a 1 - gbToLineage \
 | tawk '{ if ($2 == "") { $2 = "?"; }
           print $1, $1, $2, $3, $4, "", $6, $7, $8; }' \
 | join -t$'\t' -o 1.2,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9 idToName - \
 | uniq \
     >> gisaidAndPublic.$today.metadata.tsv
 # COG-UK metadata:
-if [ -e $cogUkDir/nextclade.tsv ]; then
-    sort $cogUkDir/nextclade.tsv > cogUkToNextclade
+if [ -e $cogUkDir/nextclade.full.tsv.gz ]; then
+    zcat $cogUkDir/nextclade.full.tsv.gz | cut -f 1,2 | sed -re 's/"//g' | sort -u > cogUkToNextclade
 else
     touch cogUkToNextclade
 fi
 #*** Could also add sequence length to metadata from faSizes output...
 tail -n+2 $cogUkDir/cog_metadata.csv \
 | awk -F, -v 'OFS=\t' '{print $1, "", $5, $3, "", "", "", $7; }' \
 | sed -re 's/UK-ENG/England/; s/UK-NIR/Northern Ireland/; s/UK-SCT/Scotland/; s/UK-WLS/Wales/;' \
 | sort \
 | join -t$'\t' -a 1 -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,2.2,1.8 - cogUkToNextclade \
 | join -t$'\t' -o 1.2,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9 idToName - \
     >> gisaidAndPublic.$today.metadata.tsv
 # CNCB metadata:
 tail -n+2 $cncbDir/cncb.metadata.tsv \
 | tawk '{ if ($3 != "GISAID" && $3 != "GenBank" && $3 != "Genbank") {
             print $2, "", $10, $11, $9, $5, $6} }' \
 | sed -re 's@\t([A-Za-z -]+)( / [A-Za-z -'"'"']+)+\t@\t\1\t@;  s/Sapiens/sapiens/;' \
 | sort \
 | join -t$'\t' -a 1 -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,2.2 - $cncbDir/nextclade.tsv \
 | join -t$'\t' -a 1 -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,2.2 - $cncbDir/pangolin.tsv \
 | join -t$'\t' -o 1.2,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9 idToName - \
     >> gisaidAndPublic.$today.metadata.tsv
 wc -l gisaidAndPublic.$today.metadata.tsv
 zcat $gisaidDir/metadata_batch_$today.tsv.gz \
 | grep -Fwf <(grep EPI_ISL samples.$today | cut -d\| -f 2) \
 | tawk '{print $1 "|" $3 "|" $5, "", $5, $7, $15, $13, $14, $18, $19;}' \
     >> gisaidAndPublic.$today.metadata.tsv
 wc -l gisaidAndPublic.$today.metadata.tsv
-gzip -f gisaidAndPublic.$today.metadata.tsv
+pigz -p 8 -f gisaidAndPublic.$today.metadata.tsv