1345e556ff3da44f7efcf83adc5b67868e536044
angie
  Tue Feb 22 11:08:53 2022 -0800
ncov-ingest file with accession mapping is now gzipped.

diff --git src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
index dec3504..88afe9f 100755
--- src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
+++ src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
@@ -48,31 +48,32 @@
 
 gbToDate=$ncbiDir/gbToDate
 cogUkToDate=$cogUkDir/cogUkToDate
 cncbToDate=$cncbDir/cncbToDate
 
 join -t$'\t' -a 1 -1 2 -o 1.1,1.2,1.3,2.2 \
     <(sort -k2,2 $mapScriptDir/epiToPublicIdName.$today.txt) \
     <(sort $gbToDate $cncbToDate $cogUkToDate) \
 | sort -u adders - \
     > epiToPublicAndDate.$today
 
 # Look for duplicate ID swizzles relative to existing ncov-ingest mappings
 cut -f 1,2 epiToPublicAndDate.$today \
 | egrep $'\t''[A-Z][A-Z][0-9]+\.[0-9]+' \
 | sort > latestEpiToGb
-tail -n+2 ~angie/github/ncov-ingest/source-data/accessions.tsv \
+zcat ~angie/github/ncov-ingest/source-data/accessions.tsv.gz \
+| tail -n+2 \
 | tawk '{print $2, $1;}' \
 | sort > ncovEpiToGb
 wc -l latestEpiToGb ncovEpiToGb
 # But allow version updates (e.g. .1 --> .2)
 join -t$'\t' ncovEpiToGb latestEpiToGb \
 | tawk '{ ncovNoDot = substr($2, 0, index($2, ".")-1);
           latestNoDot = substr($3, 0, index($3, ".")-1);
           if (ncovNoDot != latestNoDot) {print $3, $2;} }' \
     > latestToNcov.sub
 subColumn -miss=/dev/null 2 epiToPublicAndDate.$today latestToNcov.sub tmp
 mv tmp epiToPublicAndDate.$today
 
 ln -sf epiToPublicAndDate.$today epiToPublicAndDate.latest
 
 # Now that mapping is updated, add GenBank accessions to 4th column of metadata