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This commands will make it easier to select only common items between two files being compared. If your lines start with things other than lowercase a-z, adjust this Regex appropriately. Number of lines in the output has been set to no more than 10000, and should be adjusted as needed.
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That seems a very complicated way to do intersection. Please see: http://www.pixelbeat.org/cmdline.html#sets
Use the 'comm' command
The 'comm' command is part of gnu coreutils and you have it if you have 'diff'. This is how you can do it with comm:
comm -1 -2 input.file1 input.file2