ktsirig

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...

tempest

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?

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DaWei

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.

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Pizentios

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.

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eclipsed4utoo

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