in reply to Script far too slow with large files - wisdom needed!
Hello biologistatsea,
You've gotten some good pointers, but no-one has mentioned using 'index' instead of a regex. 'index' and 'substr' are extremely fast if used properly. (Untested example).
while (my $line = <MGF>) { my $si = index( $line, 'TITLE=' ); ## Find start of 'TITL +E=' string from beginning if ( $si >= 0 ) { my $sj = index( $line, "\n", $si + 5 ); ## Get data after 'TIT +LE=' if ( $sj > $sj ) { $TI = substr( $line, $si+6, $sj-($si+6) ); +} } . . . }
Remember 'index' returns '-1' if the string is not found, so you have to test for a positive number. ( Can't do 'if ( $si )' since '-1' is 'not 0' and is TRUE.
I've seen 10 to 50 times improvement on many-GByte files. YMMV.
Regards...Ed
"Well done is better than well said." - Benjamin Franklin
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Re^2: Script far too slow with large files - wisdom needed!
by blahblahblah (Priest) on Jan 23, 2016 at 13:09 UTC |
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Seekers of Perl Wisdom