Thanks a lot, your script is great. Your solution is also a lot faster than the awk oneliner. I modified it a bit to fit my real data. 

#!/usr/bin/perl

# create names lookup table from first file
while (<>) {
    #get rid of newline in name because there might be 
    #something like >name1\stext\n in the second file
    chomp;
    $names{$_} = 1;
    last if eof;
}
$/ = "\n>";  # set input record separator

# scan second file
print ">";            # print first ">" that would be missing
while (<>) {
      
    print if /^>?([\w\d]+)/ && $names{$1};
}

[download]
The only prob I have now is, when applied to my real data a ">" sign is missing at the beginning (which I got around with a print before the second while loop) and one is too much at the end.

In reply to Re^2: awk 2 perl oneliner by Anonymous Monk
in thread awk 2 perl oneliner by space_agent

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