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Re: Perl noob struggling to loop through an array

by aitap (Curate)
on Oct 24, 2012 at 15:52 UTC ( #1000661=note: print w/replies, xml ) Need Help??

in reply to Perl noob struggling to loop through an array

Greetings, Microkorg.

The file I have read into the array is a .fasta DNA sequence file
Search for "fasta" gives many results, and nearly all threads contain links to already written code for FASTA manipulation: BioPerl fasta allBio::AlignIO::fasta

Your code is OK, but please don't use $& because it can slow down your other regexps. Catch symbols using (regexp) and use them as $number_of_catch_group, like this:

if ($line =~ /^>(.+)$/ ) { $header = $1; }
WARNING: Once Perl sees that you need one of $&, "$`", or "$'" anywhere in the program, it has to provide them for every pattern match. This may substantially slow your program. Perl uses the same mechanism to produce $1, $2, etc, so you also pay a price for each pattern that contains capturing parentheses. (To avoid this cost while retaining the grouping behaviour, use the extended regular expression "(?: ... )" instead.) But if you never use $&, "$`" or "$'", then patterns without capturing parentheses will not be penalized. So avoid $&, "$'", and "$`" if you can, but if you can't (and some algorithms really appreciate them), once you've used them once, use them at will, because you've already paid the price. As of 5.005, $& is not so costly as the other two.
Seen at perlre, right before Quoting metacharacters.

Sorry if my advice was wrong.

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