I got the following error when attempting to intersect two files. The file below is supposed to be the -a file.

Error: Unable to open file compare_me_to.txt. Exiting.

When I attempted to make it tab-delimited through Ubuntu (see code below)

perl -p -i -e 's/ /\t/g' compare_me_to.txt

I got the following error:

Can't open compare_me_to: Permission denied.

Additionally, the ownership of the folder the files are in is of my username. I can't tell if this is a bedtools problem or a Ubuntu problem or something else.

  • $\begingroup$ Just a quick check since you said you have ownership of the file... The file isn't open anywhere else (like in another shell or on desktop) when you try to convert right? $\endgroup$
    – d_kennetz
    Mar 6, 2019 at 21:18

1 Answer 1


I suspect the reason is the "-i". The following will work,

perl -pe 's/  */\t/g' compare_me_to.txt > compare_me_to.txt2

-i will want to write onto the file and create a backup. I suspect you'll have spotted chmod +w compare_me_to.txt.

Just make sure that a double space is inserted before the * character, otherwise it will go wrong. Copying and pasting will avoid this.

This is a clearer solution because it avoids missing a space character,

perl -e 's/[ ][ ]*/\t/g' compare_me_to.txt > compare_me_to.txt2

and the solution you used .. (I did on OS X), what I'd recommend is,

perl -p -e 's/[ ][ ]*/\t/g' compare_me_to.txt # to see if it works by printing on screen without altering the file

perl -i -e 's/[ ][ ]*/\t/g' compare_me_to.txt

The -i flag will alter the original file and store a backup without requiring renaming the file.

What's it doing? The regex [ ][ ]* structure is saying look a space and if one or more spaces occur adjacent to each other replace everything with a single tab. [ ]* means a "space" that is present or absent and if present it can be present an infinite number of times. If the [ ]* is by itself the command risks saying replace '' (zip) or 'space' with a tab, so tabs can appear at every '' (zilch), so tabs can appear everywhere. The "*" symbol in regex work differently to the "*" wildcard character in shell.

  • $\begingroup$ The following error appears: Can't open compare_me_to.txt: Permission denied. $\endgroup$
    – DangIt
    Mar 11, 2019 at 6:51
  • $\begingroup$ I was able to give myself permission (askubuntu.com/questions/466605/…), but the file still can't be opened when intersecting. I ran the line of code you wrote; when I opened the resulting file, every character was separated by a tab. $\endgroup$
    – DangIt
    Mar 11, 2019 at 7:20
  • $\begingroup$ Oh I know, you put a single space into the term ... its a double space followed by a *. so its ... 's/ */\t/g' ... if you only put a single space into the first / */ then it will result in tabs going everywhere. I can explain later. $\endgroup$
    – M__
    Mar 11, 2019 at 12:39
  • $\begingroup$ chmod 700 file_name is another way in, I'm surprised chmod +w file_name didn't work if you were the file owner. I assumed you knew about chown and chmod $\endgroup$
    – M__
    Mar 11, 2019 at 12:42

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.