afedd6d0dae5767b8ee9041119d72a65360f77e0
angie
  Wed Oct 4 17:46:28 2023 -0700
Strip stuff past the accession in headers when making fasta for pangolin.

diff --git src/hg/utils/otto/sarscov2phylo/getNcbi.sh src/hg/utils/otto/sarscov2phylo/getNcbi.sh
index bf672dd..f96a26b 100755
--- src/hg/utils/otto/sarscov2phylo/getNcbi.sh
+++ src/hg/utils/otto/sarscov2phylo/getNcbi.sh
@@ -122,31 +122,33 @@
 conda activate pangolin
 set -x
 runPangolin() {
     fa=$1
     out=$fa.pangolin.csv
     logfile=$(mktemp)
     pangolin -t 4 $fa --skip-scorpio --outfile $out > $logfile 2>&1
     rm $logfile
 }
 export -f runPangolin
 if [ -e ../ncbi.latest/lineage_report.csv ]; then
     cp ../ncbi.latest/lineage_report.csv linRepYesterday
     tail -n+2 linRepYesterday | sed -re 's/^([A-Z]+[0-9]+\.[0-9]+).*/\1/' | sort \
         > pangolin.prev.names
     comm -23 gb.names pangolin.prev.names > pangolin.names
-    faSomeRecords <(xzcat genbank.fa.xz) pangolin.names pangolin.fa
+    faSomeRecords <(xzcat genbank.fa.xz) pangolin.names stdout \
+    | sed -re '/^>/  s/^>([A-Z]{2}[0-9]{6}\.[0-9]+) \|[^,]+/>\1/;' \
+        > pangolin.fa
     pangolin --analysis-mode pangolearn pangolin.fa >& pangolin.log
     tail -n+2 lineage_report.csv >> linRepYesterday
     mv linRepYesterday lineage_report.csv
     rm -f pangolin.fa
 else
     splitDir=splitForPangolin
     rm -rf $splitDir
     mkdir $splitDir
     faSplit about <(xzcat genbank.fa.xz) 30000000 $splitDir/chunk
     find $splitDir -name chunk\*.fa \
     | parallel -j 10 "runPangolin {}"
     head -1 $(ls -1 $splitDir/chunk*.csv | head -1) > lineage_report.csv
     for f in $splitDir/chunk*.csv; do
         tail -n+2 $f >> lineage_report.csv
     done