d6677c2b706a2424e70bcacd517d8a61f4b39f20
angie
  Wed Apr 21 15:09:20 2021 -0700
Apparently GISAID sequence names can have apostrophes too.  Strip out more troublemaking characters.

diff --git src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
index 58060e4..1bd7e1a 100755
--- src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
+++ src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
@@ -6,34 +6,35 @@
 #	kent/src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
 
 # Make nextfasta and nextmeta substitute files from chunks of downloaded GISAID sequences
 
 lastRealNextmeta=metadata_2020-12-08_20-35.tsv.gz
 
 today=$(date +%F)
 
 # Run pangolin and nextclade on any chunks that need it
 cd /hive/users/angie/gisaid/chunks
 make
 
 cd /hive/users/angie/gisaid
 # Glom all the chunks together.
 # Remove initial "hCoV-19/" and remove spaces a la nextmeta (e.g. "Hong Kong" -> "HongKong").
+# Strip single quotes (e.g. "Cote d'Ivoire" --> "CotedIvoire").
 # Also remove a stray comma in a name that caused Newick parsing error ("Hungary/US-32533w,/2020").
 # Keep the strain|epiId|date "full names".
 time xzcat chunks/gisaid_epi_isl_*.fa.xz \
-| sed -re 's@^>hCo[Vv]-19/+@>@; s/ //g; s/,//;  s/\r$//;' \
+| sed -re 's@^>hCo[Vv]-19/+@>@;  s/[ '"'"',()]//g;  s/\r$//;' \
 | xz -T 50 \
     > gisaid_fullNames_$today.fa.xz
 
 # Make tmp files with a fullName key and various columns that we'll join together.
 fastaNames gisaid_fullNames_$today.fa.xz \
 | awk -F\| -vOFS="\t" '{print $0, $1, $2, $3;}' \
 | sort \
     > tmp.first3
 # Sequence length
 faSize -detailed  <(xzcat gisaid_fullNames_$today.fa.xz) | sort > tmp.lengths
 # Lineage & clade assignments
 sort chunks/pangolin.tsv \
     > tmp.lineage
 sort chunks/nextclade.tsv \
     > tmp.clade