Search avoiding special characters

Shell Programming and Scripting
1

Hi all,

I have a list which I want to search in another file.
I can do that using
grep -f

but the search is failing due to special characters, how do I solve this?

One row in that list is

amino-acid permease inda1 [Pyrenophora tritici-repentis  Pt-1C-BFP]gb|EDU41782.1| amino-acid permease inda1 [Pyrenophora  tritici-repentis Pt-1C-BFP]

Input file to be searched

comp1538736c0_seEON956710       5821833 putative amino-acid permease inda1 protein [Togninia minima UCRPA7]     1e-114  418     0       2       736     97      342     89.8%   80.1%
comp1538234c2_seEON956710       582.455 putative amino-acid permease inda1 protein [Togninia minima UCRPA7]     3e-18   96.7    2       2       229     338     413     71.1%   65.8%
comp1538600c3_seXP_001939063    5733127 amino-acid permease inda1 [Pyrenophora tritici-repentis Pt-1C-BFP]gb|EDU41782.1| amino-acid permease inda1 [Pyrenophora tritici-repentis Pt-1C-BFP]     5e-36   155     2       233     598     448 573      69.8%   59.5%
2

In bash:

#!/bin/bash

declare -A ARR
while read line
do
        ARR["$line"]="$line"
done < file1


while read line
do
        for k in "${ARR[@]}"
        do
                [[ "$line" =~ "$k" ]] && echo "$line"
        done
done < file2

Input

$ cat file1
amino-acid permease inda1 [Pyrenophora tritici-repentis  Pt-1C-BFP]gb|EDU41782.1| amino-acid permease inda1 [Pyrenophora  tritici-repentis Pt-1C-BFP]

$ cat file2
comp1538736c0_seEON956710       5821833 putative amino-acid permease inda1 protein [Togninia minima UCRPA7]     1e-114  418     0       2       736     97      342     89.8%   80.1%
comp1538234c2_seEON956710       582.455 putative amino-acid permease inda1 protein [Togninia minima UCRPA7]     3e-18   96.7    2       2       229     338     413     71.1%   65.8%
comp1538600c3_seXP_001939063    5733127 amino-acid permease inda1 [Pyrenophora tritici-repentis  Pt-1C-BFP]gb|EDU41782.1| amino-acid permease inda1 [Pyrenophora  tritici-repentis Pt-1C-BFP]     5e-36   155     2       233     598     448 573      69.8%   59.5%

Output

$ ./look.bash
comp1538600c3_seXP_001939063    5733127 amino-acid permease inda1 [Pyrenophora tritici-repentis  Pt-1C-BFP]gb|EDU41782.1| amino-acid permease inda1 [Pyrenophora  tritici-repentis Pt-1C-BFP]     5e-36   155     2       233     598     448 573      69.8%   59.5%
3

-F -f tells grep to consider them fixed strings, instead of regular expressions.