I am not sure I understand your points - so to clarify:

listing above was posted as pseudo code and not the actual code run - for $string1 and $string2 in the test case I put the literal strings of interest in place (and have updated to illustrate) I used what I found interesting for my specific situation and I left it generic when posting the code example above because I thought that would be more useful - I understand your point re: my $str... and now that works properly if I use your qr update (and I get the same times). This is not a useful or valid benchmark?

my input file was: 

RH_MEa0001bA09_1    1253    871    10    GGAGAGGGGTCGAATTTCTC...
RH_MEa0001bB03_1    553    104    12    GTCCGTTGCAACAAAAGTGA...
RH_MEa0001bC11_1    1160    385    12    TGGGGTTGAAGAAAGGTTNG...
RH_MEa0001bG06_1    710    14    18    Invalid starting position (14)
RH_MEa0001bG06_2    710    34    10    GGGGGACACCTTCTCTCTCT...
RH_MEa0001bG06_3    710    51    10    GGGGGACACCTTCTCTCTCT... etc

[download]

since diff boxes have different performance depending on input_files, strings, mem., proc. etc - I guess it is better to list relative results instead of specifics ... is it just luck that your results confirm the general reason I posted, that lookahead grep is the fastest (accurate) solution?

In reply to Re^4: grep for lines containg two variables by l3v3l
in thread grep for lines containg two variables by smoss74

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