Answers.Body: <p>I suspect the reason is the "-i". The following will work,</p>
  
  <pre><code>perl -pe 's/  */\t/g' compare_me_to.txt &gt; compare_me_to.txt2
  </code></pre>
  
  <p>-i will want to write onto the file and create a backup. I suspect you'll have spotted <code>chmod +w compare_me_to.txt</code>.</p>
  
  <p>Just make sure that a double space is inserted before the * character, otherwise it will go wrong. Copying and pasting will avoid this.</p>
  
  <hr>
  
  <p>This is a clearer solution because it avoids missing a space character,</p>
  
  <pre><code>perl -e 's/[ ][ ]*/\t/g' compare_me_to.txt &gt; compare_me_to.txt2
  </code></pre>
  
  <p>and the solution you used .. (I did on OS X), what I'd recommend is,</p>
  
  <pre><code>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
  </code></pre>
  
  <p>The  -i flag will alter the original file and store a backup without requiring renaming the file.</p>
  
  <p><strong>What's it doing?</strong>
  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.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-03-11T06:51:11.977Z
Answers.Text: The following error appears: `Can't open compare_me_to.txt: Permission denied.`
Answers.UserDisplayName: DangIt
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-03-11T07:20:37.190Z
Answers.Text: I was able to give myself permission (https://askubuntu.com/questions/466605/cannot-open-output-file-permission-denied), 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.
Answers.UserDisplayName: DangIt
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-03-11T12:39:24.943Z
Answers.Text: 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.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-03-11T12:42:13.133Z
Answers.Text: 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
Answers.UserDisplayName: M__
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Answers.CreationDate: 2019-03-07T03:00:30.303Z
Answers.LastActivityDate: 2019-03-11T17:39:16.347Z
Answers.LastEditDate: 2019-03-11T17:39:16.347Z
Answers.UserDisplayName: M__
Body: <p>I got the following error when attempting to intersect two files. The file below is supposed to be the -a file.</p>
  
  <pre><code>Error: Unable to open file compare_me_to.txt. Exiting.
  </code></pre>
  
  <p>When I attempted to make it tab-delimited through Ubuntu (see code below)</p>
  
  <pre><code>perl -p -i -e 's/ /\t/g' compare_me_to.txt
  </code></pre>
  
  <p>I got the following error:</p>
  
  <pre><code>Can't open compare_me_to: Permission denied.
  </code></pre>
  
  <p>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.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-03-06T21:18:44.657Z
Comments.Text: 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?
Comments.UserDisplayName: d_kennetz
Tags: <bedtools>
Title: bedtools unable to open file despite being tab-delimited
ThreadText: # bedtools unable to open file despite being tab-delimited
  
  (Asked by: username_0 on 2019-03-06)
  
  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.
  
  **Tags:** bedtools
  
  > **Comments:**
  > **username_1**: 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?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2019-03-07. Score: 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.
  
  > **Comments:**
  > **username_0**: The following error appears: `Can't open compare_me_to.txt: Permission denied.`  
  > **username_0**: I was able to give myself permission (https://askubuntu.com/questions/466605/cannot-open-output-file-permission-denied), 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.  
  > **username_2**: 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.  
  > **username_2**: 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  
  
  ---
  
  