Question

I have a text file which contains protein sequences(200 sequences) as shown below.

>ptn1
AAGHM
>ptn2
MGLKKRR

I need to give the following values to each character of the seqence and has to find the average of each sequence.

A= 0.2, G= 0.5, L=0.14, M= 0.70, R= 0.55, C=0.48, H= 1.00 , K=0.4

Desired output

ptn1  - 0.52
ptn2  - 0.462

How can I do this with awk or with python?

your suggestions would be appreciated

Answer 1

Needs gawk for FS=""
http://www.gnu.org/software/gawk/manual/html_node/Single-Character-Fields.html#Single-Character-Fields
Usage:
awk -f foo.awk foo.txt

BEGIN {
    FS=""
    k["A"]=0.2; k["G"]=0.5; k["L"]=0.14; k["M"]=0.70
    k["R"]=0.55; k["C"]=0.48; k["H"]=1.00; k["K"]=0.4
}

/^>/{
    $1=""
    name=$0
    next
}

{
    s=0
    for (i=1; i<=NF; i++) {
      s+=k[$(i)]
    }
    printf "%s - %.3f\n", name, s/NF
}