Confused with strings...

ktsirig · January 11th, 2006, 04:59 AM

Hi all!
I have this assignment to give in Biology class and I am stuck.

Assignment:
I am given a sequence of letters, say:

XXXXXXABCDXXXXXXXX

and I am interested in part ABCD, which represents letters #7-#10 as you can see.

I am then given the same sequence, which now contains characters like * and !(only these 2 are allowed),
say:

XX**XXX!!!X**AB*!C*DXX*!!!XXX**XXX

and I want to find out which letters now represent the part ABCD.
If you count, you see that ABCD is now letters #14-#20 [4*and! were added prior to A and 10 prior to D]

What I think must be done is:
1) check how many (if any) * or/and ! were added prior to start letter A(#7)
2) check how many (if any) * or/and ! were added prior to end letter D(#10)
3) add all * and/or ! to starting and ending letter of part ABCD

Has anyone got any hints to give me as to which functions of Perl will be useful for this problem?

grahame · January 11th, 2006, 02:02 PM

Quote:

Originally Posted by ktsirig

Has anyone got any hints to give me as to which functions of Perl will be useful for this problem?

Can'y you just use a regular expression to grab out the section you want and then see how long your PREMATCH and MATCH strings are? Something like:

Code:

$seq = "XX**XXX!!!X**AB*!C*DXX*!!!XXX**XXX";
$seq =~ /A[!*]*B[!*]*C[!*]*D/;
$to = length($&) - 1 + ($from = length($'));
print "from $from to $to\n";