/usr/bin/amino-acid-composition is in ncbi-entrez-direct 7.40.20170928+ds-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | #!/bin/bash -norc
abbrev=( Ala Asx Cys Asp Glu Phe Gly His Ile \
Xle Lys Leu Met Asn Pyl Pro Gln Arg \
Ser Thr Sec Val Trp Xxx Tyr Glx )
AminoAcidComp() {
local count
while read num lttr
do
idx=$(printf %i "'$lttr'")
ofs=$((idx-97))
count[$ofs]="$num"
done <<< "$1"
for i in {0..25}
do
echo -e "${abbrev[$i]}\t${count[$i]-0}"
done |
sort
}
while read seq
do
comp="$(echo "$seq" | tr A-Z a-z | sed 's/[^a-z]//g' | fold -w 1 | sort-uniq-count)"
AminoAcidComp "$comp"
done
|