Perl substrings
 

Hello everybody,
I have been dealing with this problem in PERL a few days now, and it has get into my nerves, so, if anyone has a hint on how to procceed, it would be more than welcome.
Say you have one file that contains a sequence of letters, eg :
SGFEFHGYARSGVIMNDSGASTKSGAYITPAGETGGAIGRLGNQADTYVEMNLEHKQTLDN [file 1]

the same sequence is also in the [file 2], but, with "." and "-" in it, like:
...---SGFEF....HG-.--YARSGVI---MNDSGAS..--TKSGAY--....--ITPAG--ETGGAI..GRLGN--Q..AD---TY--V..EMNL--EHKQTLDN [file 2]

Let's say I want to check how two substrings (namely SGASTK and GNQADT) have become in file 2 compared to what they were in file1.

I see that SGASTK, that was substring 19-24 in file1 is now SGAS..--TK and substring 36-41.
GNQADT which was substring 42-48 in file1 is now GN--Q..AD---T and substring 76-82.

My question is how can i find the old substrings from file 1 in file 2 and how can i store the new begginings and endings of the new substrings in file2...

I have no clue.

So, did you think of this problem yourself or is it a homework problem which the Forum Rules forbid you from posting?

Well, your description of what you need absolutely sucks. If I understand you, I would pull off the seach for the garfled substring by treating '.' and '-' as nonexistent symbols (ignored in comparisons), find the substring, and Bob's yer auntie. If it's homework, and you're explaining it jus' lak de teacher did, run like hell.

yeah DaWei is about right, just strip off the . and -. Then it's really just a simple regular expression search.

i doubt that this is a homework question, since there are ~very~ few schools that teach perl.

i would use the substitution method and then compare the two files.