bash - Read columns from a file into variables and use for substitute values in another file -

i have following file : input.txt

b73_chr10   w22_chr9 w22_chr7    w22_chr10 w22_chr8    w22_chr8 

i have written following code(given below) read first , second column , substitute values of first column values in second column in output.conf file .for example, change value b73_chr10 w22_chr9,w22_chr7 w22_chr10,w22_chr8 w22_chr8 , keep doing values till end.

value1=$(echo $line| awk -f\ '{print $1}' input.txt) value2=$(echo $line| awk -f\ '{print $2}' input.txt) sed -i '.bak' 's/$value1/$value2/g' output.conf  cat output.conf 

output.conf

    <rules>     <rule>     condition =between(b73_chr10,w22_chr1)     color = ylgn-9-seq-7     flow=continue     z=9     </rule>     <rule>     condition =between(w22_chr7,w22_chr2)     color = blue     flow=continue     z=10     </rule>     <rule>     condition =between(w22_chr8,w22_chr3)     color = vvdblue     flow=continue     z=11     </rule>     </rules> 

i tried commands(as above),but leaving blank file me.can guide went wrong ?

i suspect sed wrong tool this. can you're asking in bash alone:

#!/usr/bin/env bash  # declare associative array (requires bash 4) declare -a repl=()  # step through our replacement file, recording array. while read that;   repl["$this"]="$that" done < inp1  # read input file, replacing things strings noted in array. while read line;   string in "${!repl[@]}";     line="${line/$string/${repl[$string]}}"   done   echo "$line" done < circos.conf 

this approach of course oversimplified , therefore shouldn't used verbatim -- you'll want make sure you're editing lines want edit (verifying match /condition =between/ example). note because solution uses associative array (declare -a ...), depends on bash version 4.

if solve awk, same basic principle apply:

#!/usr/bin/awk -f  # collect tranlations first file. nr==fnr { repl[$1]=$2; next }  # step through input file, replacing required. {   ( string in repl ) {     sub(string, repl[string])   } }  # , print. 1 

you'd run first argument being translation file, , second being input file:

$ ./thisscript translations.txt circos.conf