Identifying and removing null characters in UNIX - unix

Question

I have a text file containing unwanted null characters (ASCII NUL, \0). When I try to view it in vi I see ^# symbols, interleaved in normal text. How can I:
Identify which lines in the file contain null characters? I have tried grepping for \0 and \x0, but this did not work.
Remove the null characters? Running strings on the file cleaned it up, but I'm just wondering if this is the best way?

Answer 1

I’d use tr:
tr < file-with-nulls -d '\000' > file-without-nulls
If you are wondering if input redirection in the middle of the command arguments works, it does. Most shells will recognize and deal with I/O redirection (<, >, …) anywhere in the command line, actually.

Answer 2

Use the following sed command for removing the null characters in a file.
sed -i 's/\x0//g' null.txt
this solution edits the file in place, important if the file is still being used. passing -i'ext' creates a backup of the original file with 'ext' suffix added.

Answer 3

A large number of unwanted NUL characters, say one every other byte, indicates that the file is encoded in UTF-16 and that you should use iconv to convert it to UTF-8.

Answer 4

I discovered the following, which prints out which lines, if any, have null characters:
perl -ne '/\000/ and print;' file-with-nulls
Also, an octal dump can tell you if there are nulls:
od file-with-nulls | grep ' 000'

Answer 5

If the lines in the file end with \r\n\000 then what works is to delete the \n\000 then replace the \r with \n.
tr -d '\n\000' <infile | tr '\r' '\n' >outfile

Answer 6

Here is example how to remove NULL characters using ex (in-place):
ex -s +"%s/\%x00//g" -cwq nulls.txt
and for multiple files:
ex -s +'bufdo!%s/\%x00//g' -cxa *.txt
For recursivity, you may use globbing option **/*.txt (if it is supported by your shell).
Useful for scripting since sed and its -i parameter is a non-standard BSD extension.
See also: How to check if the file is a binary file and read all the files which are not?

Answer 7

I used:
recode UTF-16..UTF-8 <filename>
to get rid of zeroes in file.

Answer 8

I faced the same error with:
import codecs as cd
f=cd.open(filePath,'r','ISO-8859-1')
I solved the problem by changing the encoding to utf-16
f=cd.open(filePath,'r','utf-16')

Answer 9

Remove trailing null character at the end of a PDF file using PHP, . This is independent of OS
This script uses PHP to remove a trailing NULL value at the end of a binary file, solving a crashing issue that was triggered by the NULL value. You can edit this script to remove all NULL characters, but seeing it done once will help you understand how this works.
Backstory
We were receiving PDF's from a 3rd party that we needed to upload to our system using a PDF library. In the files being sent to us, there was a null value that was sometimes being appended to the PDF file. When our system processed these files, files that had the trailing NULL value caused the system to crash.
Originally we were using sed but sed behaves differently on Macs and Linux machines. We needed a platform independent method to extract the trailing null value. Php was the best option. Also, it was a PHP application so it made sense :)
This script performs the following operation:
Take the binary file, convert it to HEX (binary files don't like exploding by new lines or carriage returns), explode the string using carriage return as the delimiter, pop the last member of the array if the value is null, implode the array using carriage return, process the file.
//In this case we are getting the file as a string from another application.
// We use this line to get a sample bad file.
$fd = file_get_contents($filename);
//We trim leading and tailing whitespace and convert the string into hex
$bin2hex = trim(bin2hex($fd));
//We create an array using carriage return as the delminiter
$bin2hex_ex = explode('0d0a', $bin2hex);
//look at the last element. if the last element is equal to 00 we pop it off
$end = end($bin2hex_ex);
if($end === '00') {
array_pop($bin2hex_ex);
}
//we implode the array using carriage return as the glue
$bin2hex = implode('0d0a', $bin2hex_ex);
//the new string no longer has the null character at the EOF
$fd = hex2bin($bin2hex);