5f1c3399aaa5c1bcd341470a156cb528073546d3
angie
  Thu Jan 13 11:39:32 2022 -0800
Uniqueify to prevent dups from several possible sources.

diff --git src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
index b29043f..235aa79 100755
--- src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
+++ src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
@@ -21,54 +21,54 @@
 
 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/\r$//;' \
 | xz -T 8 \
     > gisaid_fullNames_$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, $3;}' \
-| sort \
+| sort -u \
     > tmp.first3
 # Sequence length
-faSize -detailed  <(xzcat gisaid_fullNames_$today.fa.xz) | sort > tmp.lengths
+faSize -detailed  <(xzcat gisaid_fullNames_$today.fa.xz) | sort -u > tmp.lengths
 # Lineage & clade assignments
-sort chunks/pangolin.tsv \
+sort -u chunks/pangolin.tsv \
     > tmp.lineage
-sort chunks/nextclade.tsv \
+sort -u chunks/nextclade.tsv \
     > tmp.clade
 # Countries -- go back to unstripped sequence names:
 xzcat chunks/gisaid_epi_isl_*.fa.xz \
 | grep ^\> \
 | sed -re 's@^>hCo[Vv]-19/+@@;' \
 | $scriptDir/gisaidNameToCountry.pl \
-| sort \
+| sort -u \
     > tmp.country
 
 # Join locally computed fields and sort by EPI ID for joining with latest real nextmeta
 join -t$'\t' -a 1 tmp.first3 tmp.lengths \
 | join -t$'\t' -a 1 -o 1.1,1.2,1.3,1.4,1.5,2.2 - tmp.clade \
 | join -t$'\t' -a 1 -o 1.1,1.2,1.3,1.4,1.5,1.6,2.2 - tmp.lineage \
 | join -t$'\t' -a 1 -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,2.2 - tmp.country \
 | tawk '{print $3, $2, $4, $5, $6, $7, $8;}' \
-| sort \
+| sort -u \
     > tmp.epiToLocalMeta
 # Join with latest real nextmeta and put locally computed fields in nextmeta column positions.
 # Last real nextmeta has 27 columns.  These are the columns we can fill in:
 #1       strain
 #3       gisaid_epi_isl
 #4       genbank_accession # fold in later, after updating mapping
 #5       date
 #7       country
 #14      length
 #18      Nextstrain_clade
 #19      pangolin_lineage
 # Fill in other columns from nextmeta when possible (join on EPI ID since names change over time)
 set +o pipefail
 zcat $lastRealNextmeta | head -1 \
     > metadata_batch_$today.tsv