Re: pattern match, speed problem

For matching fixed substrings index is faster. It just requires a slight modification to the code

    my $position = index $chrom, $_;
    if ( $position != -1 ) {
        # we matched
    }
[download]

Comment on Re: pattern match, speed problem Download Code

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Re^2: pattern match, speed problem by ysth (Canon) on Feb 20, 2008 at 07:37 UTC
And the large string needs to be uppercased, since the pattern match was case insensitive. -- Online Fortune Cookie Search	[reply]
Re^3: pattern match, speed problem by hipowls (Curate) on Feb 20, 2008 at 07:56 UTC
Or lower case each probe string, that's probably cheaper. Of course if the original data was all the same case then some overhead can be avoided. If the probe strings or the large string are used multiple times then it may be worthwhile preprocessing the data. `perl -pe'tr/acgt/ACGT/' -i big_string_file` [download] or `perl -pe'tr/ACGT/acgt/' -i probe_string_file` [download]	[reply] [d/l] [select]


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