a5a4f89c3230564550036f73c9821617d3ab4bac
angie
  Thu Mar 23 13:28:16 2023 -0700
No idea why I was skipping the first 3 lines of includeRecombinants.tsv rather than just the header line.

diff --git src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
index 0f948c6..3327343 100755
--- src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
+++ src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
@@ -1,322 +1,322 @@
 #!/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
 
 # Before updating the tree with new sequences, update the names used in the tree:
 # * Sequences that are already in the tree with EPI_ IDs, but that have been mapped to public IDs
 # * COG-UK sequences that are in GenBank.  Per Sam Nicholls the isolate alone is enough to identify
 #   them -- no need to match country & year which are sometimes incorrect at first.
 grep COG-UK/ $ncbiDir/ncbi_dataset.plusBioSample.tsv \
 | tawk '{print $6, $4 "/" $6 "/" $3 "|" $1 "|" $3;}' \
 | sed -re 's@COG-UK/@@g; s/United Kingdom://; s/(\/[0-9]{4})(-[0-9]+)*/\1/; s/ //g;' \
 | sort \
     > cogUkInGenBankIsolateToNewName
 fastaNames $cogUkDir/cog_all.fasta.xz > cogUk.names
 grep -Fwf <(cut -f 1 cogUkInGenBankIsolateToNewName) cogUk.names \
     > cogUkInGenBank
 set +o pipefail
 # From 2021-05-04 on there should be no more unrenamed COG-UK/ in prevNames, but doesn't hurt
 # to check.
 grep COG-UK/ prevNames \
 | awk -F\| '{print $1 "\t" $0;}' \
 | sed -re 's@COG-UK/@@;' \
 | sort \
     > cogUkInGenBankIsolateToPrevName
 set -o pipefail
 join -t$'\t' cogUkInGenBankIsolateToPrevName cogUkInGenBankIsolateToNewName \
 | cut -f 2,3 \
     > prevTree.renaming
 # Look for COG-UK isolates in prevNames that have just been added to GenBank and need to be renamed.
 # Unfortunately for now we are not getting those from $epiToPublic.
 grep -Fwf <(cut -f 1 cogUkInGenBankIsolateToNewName) prevNames \
 | awk -F\| '$3 == ""' \
 | awk -F/ '{print $2 "\t" $0;}' \
 | sort \
     > cogUkInGenBankIsolateToPrevName
 join -t$'\t' cogUkInGenBankIsolateToPrevName cogUkInGenBankIsolateToNewName \
 | cut -f 2,3 \
     >> prevTree.renaming
 # Look for names with EPI_IDs that have just today been mapped to public sequences.
 grep EPI_ISL_ prevNames \
 | awk -F\| '{print $2 "\t" $0;}' \
 | sort \
     > epiToPrevName
 set +o pipefail
 grep -Fwf <(cut -f 1 epiToPrevName) $epiToPublic \
 | grep -v COG-UK/ \
 | tawk '{if ($4 != "" && $3 == $2) { print $1, $2 "|" $4; } else if ($4 != "") { print $1, $3 "|" $2 "|" $4; }}' \
 | sort \
     > epiToNewName
 set -o pipefail
 # Argh, missing sequences in COG-UK metadata can mean that a sequence may have been added to the
 # tree both with and without EPI ID... so renaming makes a name conflict.
 # If there are any of those then prune the sequences with EPI_ID or longer dates, so renaming doesn't
 # cause conflict.
 comm -12 <(cut -f 2 epiToNewName | sort) <(sort prevNames) > epiToNewNameAlreadyInTree
 join -t$'\t' epiToPrevName <(grep -vFwf epiToNewNameAlreadyInTree epiToNewName) \
 | cut -f 2,3 \
     >> prevTree.renaming
 cp /dev/null dupsToRemove
 if [ -s epiToNewNameAlreadyInTree ]; then
     set +o pipefail
     grep -Fwf <(cut -d\| -f 1 epiToNewNameAlreadyInTree) prevNames \
     | grep EPI_ISL \
     | cat \
         >> dupsToRemove
     set -o pipefail
 fi
 # Don't rename if the final name is already in the tree; remove the dup with the old name.
 set +o pipefail
 cut -f 2 prevTree.renaming \
 | grep -Fwf - prevNames | cat \
     > alreadyThere
 grep -Fwf alreadyThere prevTree.renaming | cut -f 1 \
     >> dupsToRemove
 # And finally, sometimes there are duplicates due to country or date being corrected in COG-UK
 # metadata.
 grep -vFwf dupsToRemove prevTree.renaming \
 | cut -f 2 | sort | uniq -c | awk '$1 > 1 {print $2;}' \
 | cut -d/ -f 2 \
     > cogUkIsolateStillDup
 grep -Fwf cogUkIsolateStillDup $cogUkDir/cog_metadata.csv \
 | awk -F, '{print $1 "|" $5;}' \
     > cogDupsLatestMetadata
 grep -Fwf cogUkIsolateStillDup prevNames \
 | grep -vFwf dupsToRemove \
 | grep -vFwf cogDupsLatestMetadata \
 | cat \
     >> dupsToRemove
 set -o pipefail
 startingProtobuf=$baseProtobuf
 if [ -s dupsToRemove ]; then
     startingProtobuf=prevDupTrimmed.pb
     $matUtils extract -i $baseProtobuf -p -s dupsToRemove -o $startingProtobuf
 fi
 
 if [ -s prevTree.renaming ]; then
     $matUtils mask -r prevTree.renaming -i $startingProtobuf -o prevRenamed.pb >& rename.out
     $matUtils extract -i prevRenamed.pb -u prevNames
 else
     ln -sf $startingProtobuf prevRenamed.pb
 fi
 
 # OK, now that the tree names are updated, figure out which seqs are already in there and
 # which need to be added.
 awk -F\| '{if ($3 == "") { print $1; } else { print $2; } }' prevNames \
 | grep -E '^[A-Z]{2}[0-9]{6}\.[0-9]' > prevGbAcc
 grep -E '^(England|Northern|Scotland|Wales)' prevNames \
 | cut -d\| -f1 > prevCogUk
 awk -F\| '{if ($3 == "") { print $1; } else { print $2; } }' prevNames \
 | grep -E '^EPI_ISL_' > prevGisaid
 # Add public sequences that have been mapped to GISAID sequences to prevGisaid.
 grep -Fwf prevGbAcc $epiToPublic | cut -f 1 >> prevGisaid
 grep -Fwf prevCogUk $epiToPublic | cut -f 1 >> prevGisaid
 wc -l prev*
 
 # 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
 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
 cut -f 1 *.refBackfill > refBackfill.ids
 sort -u ../tooManyEpps.ids ../badBranchSeed.ids dropoutContam.ids refBackfill.ids \
-| grep -vFwf <(tail -n+4 $scriptDir/includeRecombinants.tsv | cut -f 1) \
+| grep -vFwf <(tail -n+2 $scriptDir/includeRecombinants.tsv | cut -f 1) \
     > exclude.ids
 
 # Get new GenBank sequences with at least $minReal non-N bases.
 # Exclude seqs in the tree with EPI IDs that that have been mapped in the very latest $epiToPublic.
 set +o pipefail
 egrep $'\t''[A-Z][A-Z][0-9]{6}\.[0-9]+' $epiToPublic \
 | grep -Fwf prevGisaid - \
 | grep -vFwf prevGbAcc \
 | cat \
     >> prevGbAcc
 set -o pipefail
 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.
 set +o pipefail
 fastaNames newGenBank.fa | grep NC_045512 >> gbTooSmall
 set -o pipefail
 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.
 comm -23 <(fastaNames $cogUkDir/cog_all.fasta.xz | sort) \
     <(cut -d, -f1 $cogUkDir/cog_metadata.csv | sort) \
     > cogFaNotMeta
 # Also exclude COG-UK sequences that have been added to GenBank (cogUkInGenBank, see above).
 xzcat $cogUkDir/cog_all.fasta.xz \
 | faSomeRecords -exclude stdin \
     <(cat prevCogUk cogFaNotMeta cogUkInGenBank exclude.ids) 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
 
 # Exclude public-mapped sequences from newGisaid:
 set +o pipefail
 fastaNames newGisaid.filtered.fa \
 | grep -Fwf - $epiToPublic \
 | cut -f 1 \
     > newGisaid.public.names
 set -o pipefail
 if [ -s newGisaid.public.names ]; then
     faSomeRecords -exclude newGisaid.filtered.fa newGisaid.public.names tmp
     mv tmp newGisaid.filtered.fa
     faSize newGisaid.filtered.fa
 fi
 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 50
 faSize $alignedFa
 
 # Now make a renaming that keeps all the prevNames and adds full names for the new seqs.
 tawk '{print $1, $1;}' prevNames > $renaming
 if [ -s newCogUk.filtered.fa ]; then
     # Sometimes all of the new COG-UK sequences are missing from cog_metadata.csv -- complained.
     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 \
     | grep COG-UK/ \
     | sed -re 's/[ |].*//' \
     | grep -Fwf - $ncbiDir/ncbi_dataset.plusBioSample.tsv \
     | tawk '{print $1, $4 "/" $6 "/" $3 "|" $1 "|" $3;}' \
     | sed -re 's@COG-UK/@@g; s/United Kingdom://; s/(\/[0-9]{4})(-[0-9]+)*/\1/; s/ //g;' \
         >> $renaming
     fastaNames newGenBank.filtered.fa \
     | grep -v COG-UK/ \
     | sed -re 's/[ |].*//' \
     | grep -Fwf - $ncbiDir/ncbi_dataset.plusBioSample.tsv \
     | tawk '{ if ($3 == "") { $3 = "?"; }
               if ($6 != "") { print $1 "\t" $6 "|" $1 "|" $3; }
               else { print $1 "\t" $1 "|" $3; } }' \
     | cleanGenbank \
     | sed -re 's/ /_/g' \
         >> $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
 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