How to modify same file in unix?

Quick and dirty trick with your current command:

(cat file.csv | tr -d ' \t\n\r' | tr '|' '\n' |sed "s/.$//" > file2.csv && mv file2.csv file.csv) 

Explanations:

Adding && mv file2.csv file csv to your command will trigger the move operation if and only if the first command finished successfully.

This being said, your current command should be simplified!!! Example: avoid using cat and pipe when you can redirect stdin

(tr -d ' \t\n\r' < file.csv | tr '|' '\n' |sed "s/.$//" > file2.csv && mv file2.csv file.csv) 

After the edit let me introduce you a inline command that will modify the file directly without creating any intermediate file, for this purpose I use sed

Input:

$ more file.csv 330000, 200000, , , xbdcb, rrrrrr, N, N, 2018-06-14,N,|, 330000, 200000, , , xbdcb, rrrrrr, N, N, 2018-06-14,N,|, 330000, 200000, , , xbdcb, rrrrrr, N, N, 2018-06-14,N,|, 330000, 200000, , , xbdcb, rrrrrr, N, N, 2018-06-14,N,|, 

Command:

$ sed -n -i.bak 'h;n;H;n;x;s/[\n ]//g;s/,|,$//;p' file.csv 

Edited file:

$ more file.csv 330000,200000,,,xbdcb,rrrrrr,N,N,2018-06-14,N 330000,200000,,,xbdcb,rrrrrr,N,N,2018-06-14,N 330000,200000,,,xbdcb,rrrrrr,N,N,2018-06-14,N 330000,200000,,,xbdcb,rrrrrr,N,N,2018-06-14,N 

Explanations:

• -n option is used to unable the default printing of sed
• -i.bak is to modify the file in-line and to take a backup .bak file if you are sure about what you do change this to -i, sed will directly modify the file without taking any backup
• h;n; -> h put the content of current line into hold buffer and go to next line n
• H;n; -> H append the current line to the hold buffer and go to next line
• x; exchange the pattern buffer and the hold buffer to perform the modification and the printing it
• s/[\n ]//g remove all spaces and EOL from the pattern buffer
• s/,|,$// remove the ,|, at the end of the line
• p print the pattern buffer

Last but not least, in case you have more empty lines that what you have showed in your example, please use:

$ sed -n -i.bak '/^ *$/!{h;n;H;x;s/[\n ]//g;s/,|,$//;p}' file.csv 

Use a temporary file. For example:

cat file.csv | tr -d " \t\n\r" | tr '|' '\n' |sed "s/.$//" > filetemp.csv && cp filetemp.csv file.csv