data_prep.sh

# multiple sequence alignment file prep for beauti 
# after completing nextstrain workflow through 'mask' steps,  
# make sure there are no duplicate strain names prior to running 
# usage: 
# ./data_prep.sh


mkdir ../monkeypox-build/results/beauti 
cp ../monkeypox-build/results/hmpxv1/metadata.tsv results/beauti/
cp ../monkeypox-build/results/hmpxv1/masked.fasta results/beauti/
cd ../monkeypox-build/results/beauti

#make new strain name col with format name_country_date
awk -F"\t" 'OFS="\t" {$1=$4"_"$7"_"$5; print}' metadata.tsv > meta.tsv

#remove spaces from strain names 
awk -F"\t" 'OFS="\t" {gsub(/[[:blank:]]/, "",$1); print}' meta.tsv > tmp && mv tmp meta.tsv

#rename column as 'strain'
awk -F"\t" 'OFS="\t" {sub(/strain_original_country_date/,"strain",$1); print}' meta.tsv > tmp && mv tmp meta.tsv 

#make key,value file kv.txt with 1st col 'accessions', 2nd col 'strain'
awk 'NR==1{OFS="\t";save=$2;print $2,$1}NR>1{print $2,$1,save}' meta.tsv > kv.txt 
awk '!($3="")' kv.txt

#replace old strain names in alignment .fasta  with new strain names 
cat masked.fasta | seqkit replace --ignore-case --kv-file <(cut -f 1,2 kv.txt) --pattern "^(\w+)" --replacement "{kv}" > align.fasta