I have many files (with a .fna extension). I need to move them, if they contain the character > a certain number of times.
I know which files contain > a certain number of times (9 times in this example) with this command.
grep -c ">" *.fna | grep ":9"
Which gives an output like this
5242_ref.fna:9
9418_ref.fna:9
But I don't know how to move those files to another folder.
Thanks.
By combining egrep (called with the -l option so that positive matches return only filenames) with xargs you can perform arbitrary commands based on text matches:
[gnubeard@mothership: ~/mver]$ ls
destination example.fna non_example.fna
[gnubeard@mothership: ~/mver]$ cat example.fna
>>>>>>>>>
[gnubeard@mothership: ~/mver]$ cat non_example.fna
<<<<<<<<<
>>
[gnubeard@mothership: ~/mver]$ egrep -l '>{9}' *.fna | xargs -I{} mv {} destination/
[gnubeard@mothership: ~/mver]$ ls
destination non_example.fna
[gnubeard@mothership: ~/mver]$ ls destination/
example.fna
Edit: This doesn't match files with a certain number of instances of a character, if they're separated by other characters or newlines. I've created this short script that should operate as desired.
#! /usr/bin/env bash
DESTINATION=./destination
MATCH_CHAR='>'
MATCH_COUNT=9
for FILE in $1; do
MATCHES=$(grep -o $MATCH_CHAR $FILE | wc -l)
if [ $MATCHES -eq $MATCH_COUNT ]; then
mv $FILE $DESTINATION
fi
done
Example:
[gnubeard@mothership: ~/mver]$ ls
destination example.fna mver non_example.fna
[gnubeard@mothership: ~/mver]$ cat example.fna
>>
>>foo>>bar>>>baz
[gnubeard@mothership: ~/mver]$ cat non_example.fna
<<<<<<<<<
>>
[gnubeard@mothership: ~/mver]$ ./mver *.fna
[gnubeard@mothership: ~/mver]$ ls destination/
example.fna
[gnubeard@mothership: ~/mver]$ ls
destination mver non_example.fna
You could use zsh with its expression-as-a-glob-qualifier to select files that only have nine such symbols:
$ hasnine() { [[ $(tr -dc '>' < "$REPLY" | wc -c) -eq 9 ]]; }
$ mv *.fna(+hasnine) location/
The first line defines a function whose purpose is to create a true/false filter for files that have nine > symbols in them. The tr command acts on its input, expected in the REPLY variable, deleting anything that is not a >, then asks wc to count the number of resulting characters, and then compares that output to 9.
The second line executes the mv command for matching *.fna files to the (example) location directory. Matching *.fna files also have to pass the expression qualifier, which is given as the name of the function we defined.
>>), does it count only once (asgrep -cwould do), or twice (as "contains > a certain number of times" would do?