This will probably do what you want:
content = fileread('samplefile.txt');
linestocopy = regexp(content, '^([^|]*\|){4}~\|.*$', 'match', 'dotexceptnewline', 'lineanchors');
newfile = fopen('copiedlines.txt', 'wt');
fprintf(newfile, strjoin(linestocopy, '\n'));
fclose(newfile);
It uses a regular expression to find all the lines that start by (any number of characters but | followed by | ) repeated four times, followed by ~|, then anything up to the end of the line.
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