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;
Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
Read Where should I post X? if you're not absolutely sure you're posting in the right place.
Please read these before you post! —
Posts may use any of the Perl Monks Approved HTML tags:
You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
- a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
Link using PerlMonks shortcuts! What shortcuts can I use for linking?
See Writeup Formatting Tips and other pages linked from there for more info.
| & || & |
| < || < |
| > || > |
| [ || [ |
| ] || ] ||