Dear All,

I need your help to correct me.

I have two files named unique.txt and Total.txt.

unique.txt file contain two columns each columns are separated by tab. Total.txt file contain: 3 columns each column separated by tab.

What I do, take each rows from unique.txt file find that in total.txt file. If present then extract entire row from total.txt and save it in new output file new_out.txt.

To do this I use shell script

#!/bin/bash
FILE=$1
while read line; do
    egrep "$line" Total.txt > new_out.txt
done < $unique.txt

I know this is very poor attempt to resolve this problem. Please help me to improve it and reach up to optimal solution.

Please help out.

Unique.txt

mitochondria_205000_225000 mitochondria_195000_215000
mitochondria_345000_365000 mitochondria_335000_355000
mitochondria_345000_365000 mitochondria_5000_25000
chloroplast_115000_128207 chloroplast_35000_55000
chloroplast_115000_128207 chloroplast_15000_35000
mitochondria_185000_205000 mitochondria_25000_45000
2_16595000_16615000 2_16585000_16605000
4_2785000_2805000 4_2775000_2795000
4_11395000_11415000 4_11385000_11405000
4_2875000_2895000 4_2865000_2885000
4_13745000_13765000 4_13735000_13755000

Total.txt

interaction1 mitochondria_205000_225000 mitochondria_195000_215000
interaction2 mitochondria_345000_365000 mitochondria_335000_355000
interaction3 mitochondria_345000_365000 mitochondria_5000_25000
interaction4 chloroplast_115000_128207 chloroplast_35000_55000
interaction5 chloroplast_115000_128207 chloroplast_15000_35000
interaction15 2_10515000_10535000 2_10505000_10525000

Waiting for your valuable suggestions