5b376b2547f4a5018823202b0379aad6a5d06c69
angie
  Wed Dec 15 19:27:39 2021 -0800
The latest nextclade adds quotes around names with spaces; strip those out.

diff --git src/hg/utils/otto/sarscov2phylo/getCogUk.sh src/hg/utils/otto/sarscov2phylo/getCogUk.sh
index 3481bbd..da24f0b 100755
--- src/hg/utils/otto/sarscov2phylo/getCogUk.sh
+++ src/hg/utils/otto/sarscov2phylo/getCogUk.sh
@@ -49,24 +49,24 @@
     faSomeRecords <(xzcat cog_all.fasta.xz) seqsForNextclade seqsForNextclade.fa
     splitDir=splitForNextclade
     rm -rf $splitDir
     mkdir $splitDir
     faSplit about seqsForNextclade.fa 30000000 $splitDir/chunk
     nDataDir=~angie/github/nextclade/data/sars-cov-2
     outDir=$(mktemp -d)
     outTsv=$(mktemp)
     for chunkFa in $splitDir/chunk*.fa; do
         nextclade -j 50 -i $chunkFa \
             --input-root-seq $nDataDir/reference.fasta \
             --input-tree $nDataDir/tree.json \
             --input-qc-config $nDataDir/qc.json \
             --output-dir $outDir \
             --output-tsv $outTsv >& nextclade.log
-        cut -f 1,2 $outTsv | tail -n+2 >> nextclade.tsv
+        cut -f 1,2 $outTsv | tail -n+2 | sed -re 's/"//g;' >> nextclade.tsv
         rm $outTsv
     done
     rm -rf $outDir
     rm -rf $splitDir
 fi
 
 rm -f $ottoDir/cogUk.latest
 ln -s cogUk.$today $ottoDir/cogUk.latest