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I endorse all the excellent improvements made by GrandFather. Some further minor tweaks follow. For removing whitespace, you could change from:

$seq =~ s/\s//g;
$seq =~ s/\s+//g;
That should be a touch more efficient and is more idiomatic -- see also perlfaq4 "How do I strip blank space from the beginning/end of a string?".

An alternative for counting the number of bases is to change from:

my $A = () = $seq =~ /A/ig;
my $A = $seq =~ tr/aA//;
Counting characters with tr seems a bit odd but is normally fastest and is idiomatic Perl -- see Quote and Quote-like Operators.

Finally, to see what actually matches in the regex, and so help you debug it, note that you could expand it a bit like this:

my @matches = $seq =~ /[AG]TG.*?T[AG][AG]/ig; print "Here are the matched parts of the string:\n"; print " '$_'\n" for @matches; my $GENE = @matches;

In reply to Re^2: How to get the correct count by eyepopslikeamosquito
in thread How to get the correct count by supriyoch_2008

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