Re: Syntax error

Just before option 2, you have written }end if. There's no such thing as an endif in Perl, you forgot to make it a comment :)

I didn't read your whole script. One advice though, instead of ($base eq 'g' or $base eq 'G') you can write (lc $base eq 'g') (see lc). That should be the easy enough to understand. Then, if you want to try matching $base against several values you can write (grep { lc $base eq $_ } 'a', 'c', 'g', 't'). Read grep on that.

A lot of Perl users would use regular expressions instead of grep and lc, you can have a look at perlretut on the subject, if you feel adventurous.

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Re^2: Syntax error by tobyink (Canon) on Feb 10, 2014 at 00:34 UTC
Or better still, lowercase `$base` as soon as you set it: `$base = lc substr($sequence, $position, 1);` [download] Then comparisons can just be like: `if ($base eq 'g' or $base eq 't') { ... }` [download] ... and you don't need to worry about capital letters at all. `use Moops; class Cow :rw { has name => (default => 'Ermintrude') }; say Cow->new->name`	[reply] [d/l] [select]
Re^3: Syntax error by Eily (Monsignor) on Feb 10, 2014 at 09:21 UTC
Yeah, I guess it might have been a better idea to look at least a little more through the code before giving advice :). I just commented on the big obvious thing that jumped on my face, but I'm sure there is more than one way to improve it (that does sound perlish already :D).	[reply]
Re^2: Syntax error by Anonymous Monk on Feb 10, 2014 at 01:35 UTC
Right. Furthermore, the perlish way is to avoid iterating over characters, if possible. Consider this: `my $A_count = ($sequence =~ tr/Aa/Aa/);` [download]	[reply] [d/l]