Use Terminal in Unix and powerful grep command to select lines with specific characters or strings of characters or even specific combination of strings.
E.g. the file gene_exp.diff contains 2289014 lines. Each line contains multiple strings:
XLOC_000001 XLOC_000001 Lypla1 chr1:4797973-4836816 Random_without_RA Knockdown_without_RA OK 125.173 61.8913 -1.01611 6.08719 1.1491e-09 1.67416e-08 yes
To select lines containing only specific string use grep:
grep "Knockdown_without_RA" gene_exp.diff
This will select lines that contain "Knockdown_without_RA" from the file gene_exp.diff
To select lines containing specific combination of strings:
grep "Knockdown_without_RA.*Knockdown_with_RA.*OK.*yes" gene_exp.diff
This will select lines that contain strings "Knockdown_without_RA", "Knockdown_with_RA", "OK" and "yes" no matter what characters/strings are in between them (the sign .* corresponds to this).
To write the output to the less (rather then to the screen that may list the endless number of lines).
grep "Knockdown_without_RA.*Knockdown_with_RA.*OK.*yes" gene_exp.diff | less
To write the output to a file use > filename
grep "Knockdown_without_RA.*Knockdown_with_RA.*OK" gene_exp.diff > knockdown_witout_ra_vs_knockdown_with_ra.diff