change charters in a string based on vcf table data

Question

I have a long string file (string.txt) (abcdefghijklmnop) and a vcf table (file.vcf) which lools like that

position 2 4 6 10 n...
name1 a b c d
name2 x y z a
namen...

the table also contain "mis" and "het" and in this case the character should not be replaced

I want to change the characters in the specific location and store all the strings in a new file that will look like this

>name1
aacbecghidklmnop
>name2
axcyezghiaklmnop

is there a way to do it in a bash loop ?

Answer 1

Would you please try the following:

mapfile -t string < <(fold -w1 "string.txt")
# set string to an array of single characters: ("a" "b" "c" "d" ..)

while read -ra ary; do
    if [[ ${ary[0]} = "position" ]]; then
        # 1st line of file.vcf
        declare -a pos=("${ary[@]:1}")
        # now the array pos holds: (2 4 6 10 ..)
    else
        # 2nd line of file.vcf and after
        declare -a new=("${string[@]}")
        # make a copy of string to modify
        for ((i=0; i<${#pos[@]}; i++ )); do
            repl="${ary[$i+1]}"    # replacement
            if [[ $repl != "mis" && $repl != "het" ]]; then
                new[${pos[$i]}-1]="$repl"
                # modify the position with the replacement
            fi
        done
        echo ">${ary[0]}"
        (IFS=""; echo "${new[*]}")
        # print the modified array as a concatenated string
    fi
done < "file.vcf"

string.txt:

abcdefghijklmnop

file.vcf:

position 2 4 6 10
name1 a b c d
name2 x y z a
name3 i mis k l

Output:

>name1
aacbecghidklmnop
>name2
axcyezghiaklmnop
>name3
aicdekghilklmnop

I have tried to embed explanations as comments in the script above, but if you still have a question, please feel free to ask.

Hope this helps.