awk to reformat output if input file is empty, but not if file has data in it

Shell Programming and Scripting
1

The below awk improved bu @MadeInGermany, works great as long as the input file has data in it in the below format:

input

chrX	25031028	25031925	chrX:25031028-25031925	ARX	631	18
chrX	25031028	25031925	chrX:25031028-25031925	ARX	632	14
chrX	25031028	25031925	chrX:25031028-25031925	ARX	633	14
chrX	25031028	25031925	chrX:25031028-25031925	ARX	634	13
chrX	25031028	25031925	chrX:25031028-25031925	ARX	635	12

awk

awk '
# print from stored values
function prt(){
  print p1 ":" (p6start==1 ? p2 : p2+p6start) "-" p2+p6, "\t" p5
}
($4!=p4 || $6!=p6+1) {
# new sequence, print the previous sequence
  if (NR>1) prt()
  p6start=$6  
}
{
# store the values that we need later
  p1=$1
  p2=$2
  p4=$4
  p5=$5
  p6=$6
}
END { prt() }
' input | awk -F"[:-]" ' { print $1 "\t" $2 "\t" $3 "\t" $4}' > out

out

chrX	25031659	25031663 	ARX

However, when input is an empty file:

out

	0	0

I am trying to put a condition in the awk that will check for file being empty or 0 bytes and if file is not empty then the output remains the same, but if file is empty then the output is reformatted to the desired output of 4 zeros, tab-delimited . My attempt to do this is in the # check if empty below in bold. Since the process after this awk is expecting 4 tab-delimited fields I need to add this check. Thank you :).

awk '
  # print from stored values
  function prt(){
    print p1 ":" (p6start==1 ? p2 : p2+p6start) "-" p2+p6, "\t" p5
  }
  ($4!=p4 || $6!=p6+1) {
    # new sequence, print the previous sequence
    if (NR>1) prt()
    p6start=$6  
  }
  {
    # store the values that we need later
    p1=$1
    p2=$2
    p4=$4
    p5=$5
    p6=$6
  }
  END { prt() }
' file | awk -F"[:-]" '
  { print $1 "\t" $2 "\t" $3 "\t" $4}
' > out # make low coverage
# check if empty
if [ -s aFile ]; then  
else  
  output={ print "0     0     0     0" }
fi

desired out ---- four zeros separated by tabs

0	0	0     0
2

What do you mean by an empty file...a file with size zero bytes or one that is filled with zeros?

1 Like
3

Sorry, a file that is zero bytes, I also updated the post... Thank you :).

4

Hello cmccabe,

It will not work because -s Input_file test condition inside if will check if Input_file is having size more than ZERO. As follows from man test .

So if you want to do an action when Input_file is having size 0 then you could change it to as follows.

if [[ ! -s Input_file ]]
then
       echo -e "0\t0\t0\t0"
else
       echo "Input_file is having size.
fi

Thanks,
R. Singh