Taking your first .txt file as an example, let us see what your code is doing (remember that set -xv is your friend when trying to debug a shell script).

The for loop sets file to:

Code:

/home/cmccabe/Desktop/comparison/missing/F113.txt

Then you use the assignment:

Code:

    file1="/home/cmccabe/Desktop/comparison/test_tvc/${file%%.txt}.bed"

which sets file1 to:

Code:

/home/cmccabe/Desktop/comparison/test_tvc//home/cmccabe/Desktop/comparison/missing/F113.bed

and then your if statement correctly determines that there is no file with that name and skips the awk statement.

So maybe you would have more luck finding files to process (and therefore producing output), if you would change:

Code:

    file1="/home/cmccabe/Desktop/comparison/test_tvc/${file%%.txt}.bed"

to:

Code:

    file1=${file##*/}	# Strip off directory.
    file1="/home/cmccabe/Desktop/comparison/test_tvc/${file1%.txt}_tvc.bed"

I haven't even tried to figure out what your one-line awk script does, but I do note that with your sample directory listings you will be running this awk code three times and each time you run it, the output produced by the previous run will be destroyed. (Did you perhaps want >> instead of > as the redirection at the end of that script? Or maybe you want to redirect the output from the for loop to that file instead of repeatedly redirecting the output from the awk script. Which you want depends on whether you want to add to output from previous runs of your script or have each run of your script save only the results from that run.)

And, despite what greet_sed said, the if statements:

Code:

    if [[ -f $file1 ]]
    if [[ -f file1 ]]

(with or without the $) should have exactly the same effect when using the double square bracket conditional expressions. greet_sed was correct in saying that you need to use:

Code:

    if [[ -f $file1 ]]

instead of:

Code:

    if [[ -f file1 ]]

If you had been using one of the test commands:

Code:

    if [ -f "$file1" ]
    if test -f "$file1"

instead of conditional expressions, then not only would the $ be required, but also double-quotes should be added to protect against filenames containing field separation characters.