#Run this in the folder containing all of the HaMStR fa_dir folders to make a fasta file for each orthology group find -iname [0-9]\*.fa | xargs -i awk '{newfile=gensub( /.*\/([^\/]+)/, "\\1",1,FILENAME); print $0 >> "./"newfile }' {} sed -i '/|CAEEL|....|/ s/|CAEEL|/|/' *.fa sed -i '/|CAEEL|.....|/ s/|CAEEL|/|/' *.fa sed -i '/|CAEEL|......|/ s/|CAEEL|/|/' *.fa #sed -i '0,/|DROME|/s//|DROME-keep|/' *.fa sed -i '/|DROME|/,+1d' *.fa sed -i '/|SACCE|/,+1d' *.fa sed -i '/|CIOIN|/,+1d' *.fa sed -i '/|HOMSA|/,+1d' *.fa sed -i '/|CAEEL|/,+1d' *.fa #sed -i 's/|DROME-keep|/|DMEL|/g' *.fa