Hello nez,

How are you?
I hope you are doing fine

For your this solution, if you ask me IMHO we could avoid using renaming of a Input_file with system while reading Input_file itself could cause issues. Since Input_file is being read and we are renaming it.

IMHO, I would go with approach where will check for string FORMAT in line and print the rename shell command(I am hoping each Input_file should have only 1 rename because once Input_file which is being read is renamed can't be find again in system, since no same name file is existing now).

So what I am doing here is I am printing shell commands by same condition used in your provided code as follows:

Code:

awk '/FORMAT/{print "if [[ -n " s1 FILENAME s1 " ]]; then      echo " s1 "Input_file named " FILENAME " is already present." s1 "; else      mv " s1 FILENAME s1 OFS $10"; fi"}' *.vcf

For a sample file named file3 output will be as follows.

Code:

if [[ -n file3 ]]; then      echo Input_file named file3 is already present.; else      mv file3 ; fi

Now above will print rename commands, if OP is happy with above commands we could use | bash to raname them.

Code:

awk '/FORMAT/{print "if [[ -n " s1 FILENAME s1 " ]]; then      echo " s1 "Input_file named " FILENAME " is already present." s1 "; else      mv " s1 FILENAME s1 OFS $10"; fi"}' *.vcf | bash

Apologies if I missed here something, I thought to give my views here, cheers


Thanks,
R. Singh