Shell Programming and Scripting

I have a script to create a variable from a list, B.txt and then search it in another file, file.txt and then print the pattern line and next line.

Code:

#!/bin/bash
while read a
do
echo "$a" | grep -A 1 $a file.txt > $a\.txt    
done < B.txt

I always get that no such file or directory exists for any $a.txt
Any suggestions

Moderator's Comments:

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What's in B.txt? What's in file.txt?

The "echo $a" is useless, since you've told grep to look inside file.txt, not standard input. I'm not sure what its purpose was intended to be.

$a.txt should work just as well as $a\.txt.

What do you mean? The script prints those messages? Or that it doesn't create the files you want?

If $a is ever a string with spaces in it, it will split on those spaces, which will cause the string search string with spaces to make grep look for the string search inside the files "string", "with", "spaces", and "file.txt"

Quote it like "$a" to prevent it splitting.

Each $a in the B.txt are single lines that look like

Code:

GA2_0019_FC:7:1:2190:1031#0/1
file.txt looks like over a million lines of DNA sequence data called a fasta format
>GA2_0019_FC:7:1:2190:1031#0/1
CCTAGCAGATAATTTGAGCACGTTGAGCAGTAAAAC
>GA2_0019_FC:7:1:10764:1034#0/1
CAGTCAAATAATAATATCAGCAAGCCACCAAAAAAA
>GA2_0019_FC:7:1:11778:1033#0/1
CGTCACGACCAACGAATTCCTTGAACTTCAAGAGCT

Each output line for each $a looks like

Code:

program.sh: line 4: GA2_0019_FC:7:1:2190:1031#0/1.txt: No such file or directory

When I remove the > $a.txt from line 4, then the program works and sends it to stdout. The problem is with the redirection but I can't seem to get it to redirect to a file

are you telling you want to create different files for each search with $a.txt?

--ahamed

Hello ahamed101. You are correct. I want to make a subset of $a.txt files from the larger file.txt. The problem is that the program only works to stdout but won't work when directed output to a file.

You won't be able to create a file with the character "/" present in the file name

--ahamed

Thanks. The problem was that the character / could not be tolerated in a variable used by grep. I changed it to _ and then the script worked. Thanks for all the input.