9011b709f1fa87332b94a5920062582f5a725f68
angie
  Thu Jun 22 10:17:30 2023 -0700
Watch out for empty name and date columns for COG-UKs in GenBank

diff --git src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
index 1d1fa2c..bd850a0 100755
--- src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
+++ src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
@@ -1,319 +1,319 @@
 #!/bin/bash
 set -beEu -x -o pipefail
 
 #	Do not modify this script, modify the source tree copy:
 #	kent/src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
 
 usage() {
     echo "usage: $0 prevDate today problematicSitesVcf [baseProtobuf]"
     echo "This assumes that ncbi.latest and cogUk.latest links/directories have been updated."
 }
 
 if (( $# != 3 && $# != 4 )); then
   usage
   exit 1
 fi
 
 prevDate=$1
 today=$2
 problematicSitesVcf=$3
 if [ $# == 4 ]; then
     baseProtobuf=$4
 else
     baseProtobuf=
 fi
 
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 ncbiDir=$ottoDir/ncbi.latest
 cogUkDir=$ottoDir/cogUk.latest
 cncbDir=$ottoDir/cncb.latest
 gisaidDir=/hive/users/angie/gisaid
 minReal=20000
 ref2bit=/hive/data/genomes/wuhCor1/wuhCor1.2bit
 epiToPublic=$gisaidDir/epiToPublicAndDate.latest
 
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 source $scriptDir/util.sh
 
 mkdir -p $ottoDir/$today
 cd $ottoDir/$today
 
 # If there's a version that I didn't want to push out to the main site, but wanted to be used
 # as the basis for the next day's build (for example with some extra pruning), use that:
 if [ -e $ottoDir/$prevDate/gisaidAndPublic.$prevDate.masked.useMe.pb ]; then
     prevProtobufMasked=$ottoDir/$prevDate/gisaidAndPublic.$prevDate.masked.useMe.pb
 else
     prevProtobufMasked=$ottoDir/$prevDate/gisaidAndPublic.$prevDate.masked.pb
 fi
 
 usherDir=~angie/github/usher
 usher=$usherDir/build/usher
 matUtils=$usherDir/build/matUtils
 
 renaming=oldAndNewNames
 
 if [ "$baseProtobuf" == "" ]; then
     baseProtobuf=$prevProtobufMasked
 fi
 
 # Make lists of sequences already in the tree.
 $matUtils extract -i $baseProtobuf -u prevNames
 
 # First, in order to catch & remove duplicates and update names that have changed, extract the
 # accession from every name in the tree.
 awk -F\| '{ if ($3 == "") { print $1 "\t" $0; } else { print $2 "\t" $0; } }' prevNames \
 | subColumn 1 -miss=/dev/null stdin <(cut -f 1,2 $epiToPublic) stdout \
 | sort \
     > prevIdToName
 # Arbitrarily pick one of each duplicated ID to keep in the tree
 sort -k1,1 -u prevIdToName > prevIdToNameDeDup
 # Remove whichever duplicated items were not arbitrarily chosen to remain
 comm -23 prevIdToName prevIdToNameDeDup | cut -f 2 > prevNameToRemove
 # Also remove items for which we have no metadata (i.e. they were removed from repository,
 # or .1 was replaced by .2 etc.)
 cut -f 1 prevIdToNameDeDup | grep -E '^[A-Z]{2}[0-9]{6}\.[0-9]+' > gb.acc
 comm -13 <(cut -f 1 $ncbiDir/ncbi_dataset.plusBioSample.tsv) gb.acc > gb.removed.acc
 if [ -s gb.removed.acc ]; then
     grep -Fwf gb.removed.acc prevIdToName | cut -f 2 >> prevNameToRemove
 fi
 cut -f 1 prevIdToNameDeDup | grep -E '^EPI_ISL_' > epi.acc
 comm -13 <(zcat $gisaidDir/metadata_batch_$today.tsv.gz | cut -f 3 | sort) epi.acc > epi.removed.acc
 if [ -s epi.removed.acc ]; then
     grep -Fwf epi.removed.acc prevIdToName | cut -f 2 >> prevNameToRemove
 fi
 cut -f 1 prevIdToNameDeDup | grep -E '^(England|Northern|Scotland|Wales)' > cog.acc
 comm -13 <(cut -d, -f 1 $cogUkDir/cog_metadata.csv | sort) cog.acc > cog.removed.acc
 if [ -s cog.removed.acc ]; then
     grep -Fwf cog.removed.acc prevIdToName \
     | grep -vE '^([A-Z]{2}[0-9]{6}\.[0-9]+|EPI_ISL_)' \
     | cut -f 2 >> prevNameToRemove
 fi
 cut -f 1 prevIdToNameDeDup \
 | grep -vE '^([A-Z]{2}[0-9]{6}\.[0-9]+|EPI_ISL_|England|Northern|Scotland|Wales)' \
     > cncb.acc
 comm -13 <(cut -f 2 $cncbDir/cncb.metadata.tsv | sort) cncb.acc > cncb.removed.acc
 if [ -s cncb.removed.acc ]; then
     grep -Fwf cncb.removed.acc prevIdToName | cut -f 2 >> prevNameToRemove
 fi
 
 # Remove duplicates and withdrawn sequences
 if [ -s prevNameToRemove ]; then
     rm -f prevDedup.pb
     $matUtils extract -i $baseProtobuf \
         -p -s <(sort -u prevNameToRemove) \
         -u prevDedupNames \
         -o prevDedup.pb
 else
     ln -sf $baseProtobuf prevDedup.pb
     $matUtils extract -i prevDedup.pb -u prevDedupNames
 fi
 
 function gbAccCogRenaming {
     # pipeline: one INSDC accession per line of stdin, acc to full name if COG-UK on stdout
     grep -Fwf - $ncbiDir/ncbi_dataset.plusBioSample.tsv \
     | grep COG-UK/ \
-    | tawk '{print $1, $4 "/" $6 "/" $3 "|" $1 "|" $3;}' \
+    | tawk '{ if ($4 != "") { print $1, $4 "/" $6 "/" $3 "|" $1 "|" $3; } else { if ($3 != "") { print $1, $6  "/" $3 "|" $1 "|" $3; } else { print $1, $6 "|?"; } } }' \
     | sed -re 's@COG-UK/@@g; s/United Kingdom://; s/(\/[0-9]{4})(-[0-9]+)*/\1/; s/ //g;'
 }
 
 function gbAccNonCogRenaming {
     # pipeline: one INSDC accession per line of stdin, acc to full name if non-COG-UK on stdout
     grep -Fwf - $ncbiDir/ncbi_dataset.plusBioSample.tsv \
     | grep -v COG-UK/ \
     | cleanGenbank \
     | tawk '{ if ($3 == "") { $3 = "?"; }
               if ($6 != "") { print $1 "\t" $6 "|" $1 "|" $3; }
               else { print $1 "\t" $1 "|" $3; } }' \
     | sed -re 's/ /_/g'
 }
 
 # To update names that have changed and simplify detection of new sequences to add, relate to acc.
 # Strip country and year from COG-UK names to get COG acc.
 awk -F\| '{ if ($3 == "") { print $1 "\t" $0; } else { print $2 "\t" $0; } }' prevDedupNames \
 | subColumn 1 -miss=/dev/null stdin <(cut -f 1,2 $epiToPublic) stdout \
 | sed -re 's@^(England|Northern_?Ireland|Scotland|Wales)/([A-Z]+[_-]?[A-Za-z0-9]+)/[0-9]+@COG:\2@;' \
 | sort \
     > accToPrevDedupName
 
 # Break down accs by source -- we will need those both for renaming acc to full name and for
 # figuring out which seqs the tree already has vs. which are new.
 cut -f 1 accToPrevDedupName | grep -E '^[A-Z]{2}[0-9]{6}\.[0-9]+' > prevGbAcc
 cut -f 1 accToPrevDedupName | grep -E '^COG:' | sed -re 's/^COG://;' > prevCogUk
 cut -f 1 accToPrevDedupName | grep -E '^EPI_ISL_' > prevGisaid
 cut -f 1 accToPrevDedupName | grep -vE '^([A-Z]{2}[0-9]{6}\.[0-9]+|COG:|EPI_ISL_)' > prevCncb
 
 # GenBank renaming has both COG-UK and non-COG-UK versions:
 gbAccCogRenaming < prevGbAcc > accToNewName
 gbAccNonCogRenaming < prevGbAcc >> accToNewName
 # Restore the COG:isolate format for non-GenBank COG-UK sequences:
 grep -Fwf prevCogUk $cogUkDir/cog_metadata.csv \
 | awk -F, '{print $1 "\t" $1 "|" $5;}' \
 | sed -re 's@^(England|Northern_?Ireland|Scotland|Wales)/([A-Z]+[_-]?[A-Za-z0-9]+)/[0-9]+@COG:\2@;' \
     >> accToNewName
 # GISAID:
 zcat $gisaidDir/metadata_batch_$today.tsv.gz \
 | grep -Fwf prevGisaid \
 | tawk '$3 != "" {print $3 "\t" $1 "|" $3 "|" $5;}' \
     >> accToNewName
 # CNCB:
 grep -Fwf prevCncb $cncbDir/cncb.metadata.tsv \
 | cleanCncb \
 | sed -re 's/ /_/g;' \
 | tawk '{print $2 "\t" $1 "|" $2 "|" $10;}' \
     >> accToNewName
 join -t$'\t' accToPrevDedupName <(sort accToNewName) \
 | tawk '$2 != $3 {print $2, $3;}' \
     > prevDedupNameToNewName
 
 $matUtils mask -i prevDedup.pb -r prevDedupNameToNewName -o prevRenamed.pb \
     >& renaming.out
 rm renaming.out
 
 # OK, now that the tree names are updated, figure out which seqs are already in there and
 # which need to be added.
 # Add GenBank COG-UK sequences to prevCogUk so we don't add dups.
 cut -f 6 $ncbiDir/ncbi_dataset.plusBioSample.tsv | grep COG-UK | sed -re 's@^COG-UK/@@;' >> prevCogUk
 # Add public sequences that have been mapped to GISAID sequences to prevGisaid.
 cut -f 1 $epiToPublic >> prevGisaid
 wc -l prev{GbAcc,CogUk,Gisaid,Cncb}
 
 # Exclude some sequences based on nextclade counts of reversions and other-clade mutations.
 zcat $gisaidDir/chunks/nextclade.full.tsv.gz \
 | $scriptDir/findDropoutContam.pl > gisaid.dropoutContam
 zcat $ncbiDir/nextclade.full.tsv.gz \
 | $scriptDir/findDropoutContam.pl > gb.dropoutContam
 zcat $cogUkDir/nextclade.full.tsv.gz \
 | $scriptDir/findDropoutContam.pl > cog.dropoutContam
 zcat $cncbDir/nextclade.full.tsv.gz \
 | $scriptDir/findDropoutContam.pl > cncb.dropoutContam
 cut -f 1 *.dropoutContam \
 | awk -F\| '{ if ($3 == "") { print $1; } else { print $2; } }' \
     > dropoutContam.ids
 # Also exclude sequences with unbelievably low numbers of mutations given sampling dates.
 zcat $gisaidDir/chunks/nextclade.full.tsv.gz | cut -f 1,10 \
 | awk -F\| '{ if ($3 == "") { print $1 "\t" $2; } else { print $2 "\t" $3; } }' \
 | $scriptDir/findRefBackfill.pl > gisaid.refBackfill
 zcat $ncbiDir/nextclade.full.tsv.gz | cut -f 1,10 | sort \
 | join -t $'\t' <(cut -f 1,3 $ncbiDir/ncbi_dataset.plusBioSample.tsv | sort) - \
 | $scriptDir/findRefBackfill.pl > gb.refBackfill
 zcat $cogUkDir/nextclade.full.tsv.gz | cut -f 1,10 | sort \
 | join -t $'\t' <(cut -d, -f 1,5 $cogUkDir/cog_metadata.csv | tr , $'\t' | sort) - \
 | $scriptDir/findRefBackfill.pl > cog.refBackfill
 zcat $cncbDir/nextclade.full.tsv.gz | cut -f 1,10 | sort \
 | join -t$'\t' <(cut -f 2,10 $cncbDir/cncb.metadata.tsv | sort) - \
 | $scriptDir/findRefBackfill.pl > cncb.refBackfill
 cut -f 1 *.refBackfill > refBackfill.ids
 sort -u ../tooManyEpps.ids ../badBranchSeed.ids dropoutContam.ids refBackfill.ids \
 | grep -vFwf <(tail -n+2 $scriptDir/includeRecombinants.tsv | cut -f 1) \
     > exclude.ids
 
 # Get new GenBank sequences with at least $minReal non-N bases.
 xzcat $ncbiDir/genbank.fa.xz \
 | faSomeRecords -exclude stdin <(cat prevGbAcc exclude.ids) newGenBank.fa
 faSize -veryDetailed newGenBank.fa \
 | tawk '$4 < '$minReal' {print $1;}' \
     > gbTooSmall
 # NCBI also includes NC_045512 in the download, but that's our reference, so... exclude that too.
 echo NC_045512.2 >> gbTooSmall
 faSomeRecords -exclude newGenBank.fa gbTooSmall newGenBank.filtered.fa
 faSize newGenBank.filtered.fa
 
 # Get new COG-UK sequences with at least $minReal non-N bases.
 # Also exclude cog_all.fasta sequences not found in cog_metadata.csv.
 fastaNames $cogUkDir/cog_all.fasta.xz \
 | grep -vFwf prevCogUk \
 | grep -vFwf exclude.ids \
 | grep -Fwf <(cut -d, -f 1 $cogUkDir/cog_metadata.csv) \
     > newCogUk.accs
 xzcat $cogUkDir/cog_all.fasta.xz \
 | faSomeRecords stdin newCogUk.accs newCogUk.fa
 faSize -veryDetailed newCogUk.fa \
 | tawk '$4 < '$minReal' {print $1;}' \
     > cogUkTooSmall
 faSomeRecords -exclude newCogUk.fa cogUkTooSmall newCogUk.filtered.fa
 faSize newCogUk.filtered.fa
 
 # Get new GISAID sequences with at least $minReal non-N bases.
 xzcat $gisaidDir/gisaid_fullNames_$today.fa.xz \
 | sed -re 's/^>.*\|(EPI_ISL_[0-9]+)\|.*/>\1/' \
 | faSomeRecords -exclude stdin <(cat prevGisaid exclude.ids) newGisaid.fa
 faSize -veryDetailed newGisaid.fa \
 | tawk '$4 < '$minReal' {print $1;}' \
     > gisaidTooSmall
 faSomeRecords -exclude newGisaid.fa gisaidTooSmall newGisaid.filtered.fa
 faSize newGisaid.filtered.fa
 
 # Get new CNCB sequences with at least $minReal non-N bases.
 xzcat $cncbDir/cncb.nonGenBank.acc.fasta.xz \
 | faSomeRecords -exclude stdin <(cat prevCncb exclude.ids) newCncb.fa
 faSize -veryDetailed newCncb.fa \
 | tawk '$4 < '$minReal' {print $1;}' \
     > cncbTooSmall
 faSomeRecords -exclude newCncb.fa cncbTooSmall newCncb.filtered.fa
 faSize newCncb.filtered.fa
 
 cat new*.filtered.fa > new.fa
 faSize new.fa
 
 # Use Rob's script that aligns each sequence to NC_045512.2 and concatenates the results
 # as a multifasta alignment (from which we can extract VCF with SNVs):
 #conda install -c bioconda mafft
 alignedFa=new.aligned.fa
 rm -f $alignedFa
 export TMPDIR=/dev/shm
 time bash ~angie/github/sarscov2phylo/scripts/global_profile_alignment.sh \
   -i new.fa \
   -o $alignedFa \
   -t 30
 faSize $alignedFa
 
 # Now make a renaming that converts accessions back to full name|acc|year names.
 cp /dev/null $renaming
 if [ -s newCogUk.filtered.fa ]; then
     set +o pipefail
     fastaNames newCogUk.filtered.fa \
     | grep -Fwf - $cogUkDir/cog_metadata.csv \
     | awk -F, '{print $1 "\t" $1 "|" $5;}' \
         >> $renaming
     set -o pipefail
 fi
 if [ -s newGenBank.filtered.fa ]; then
     # Special renaming for COG-UK sequences: strip COG-UK/, add back country and year
     set +o pipefail
     fastaNames newGenBank.filtered.fa \
     | sed -re 's/[ |].*//' \
     | gbAccCogRenaming \
         >> $renaming
     fastaNames newGenBank.filtered.fa \
     | sed -re 's/[ |].*//' \
     | gbAccNonCogRenaming \
         >> $renaming
     set -o pipefail
 fi
 if [ -s newGisaid.filtered.fa ]; then
     zcat $gisaidDir/metadata_batch_$today.tsv.gz \
     | grep -Fwf <(fastaNames newGisaid.filtered.fa) \
     | tawk '$3 != "" {print $3 "\t" $1 "|" $3 "|" $5;}' \
         >> $renaming
 fi
 if [ -s newCncb.filtered.fa ]; then
     cleanCncb < $cncbDir/cncb.metadata.tsv \
     | sed -re 's/ /_/g;' \
     | grep -Fwf <(fastaNames newCncb.filtered.fa) \
     | tawk '{print $2 "\t" $1 "|" $2 "|" $10;}' \
         >> $renaming
 fi
 wc -l $renaming
 
 # Make masked VCF
 tawk '{ if ($1 ~ /^#/) { print; } else if ($7 == "mask") { $1 = "NC_045512v2"; print; } }' \
     $problematicSitesVcf > mask.vcf
 time cat <(twoBitToFa $ref2bit stdout) $alignedFa \
 | faToVcf -maxDiff=200 \
     -excludeFile=exclude.ids \
     -verbose=2 stdin stdout \
 | vcfRenameAndPrune stdin $renaming stdout \
 | vcfFilter -excludeVcf=mask.vcf stdin \
 | gzip -c \
     > new.masked.vcf.gz