Hi,
I am searching for indexes of substrings in larger strings. However some
of my substrings contain one character insertions/deletions/substitutions.
Here is some sample data:
#substring(s) to search for:
$substr = "AATGCTCCCCAATGAGGCA";
$substr2 = "TT##CACAAGGAACTTTTTT";
#Search for it in this string:
$str = "CTTGAGTTATTAGCTGTTTGCCCCTGGGCAAGTTGTCTCACCTCTCCGTGTTTGTTTCCTCA
+CCTATTGGACCAGGCCTATGGTTTTCAAACTGTGTTCCCTGGTGCTCTGAGACTTAGGGAAGGGGAACG
+CCCACACTGGCAAGGCTAACACAAGCCGCCATATACCCACCCCACTTCACCCACAGCACCCCCCTTTCT
+GTGTCTCATATACTGCGGGCCTATGCGA";
# the second substring is straightforward
$pos = index( $string, $substr);
I would like the 2nd substr to match as well,
despit having the # insertions.
Perl Cookbook recipe 6.13 discusses this, and suggests using
the String:Approx module. However this module returns a list
of matches and in scalar context returns the number of sucessful
matches.
In my case I need approximate index matching. So the index
function will return an answer despite finding an approximate
match. Is there such a thing? Or are there other solutions that
I am overlooking? Thank you for your help.
