Friends,
I have a problem in getting substring according to some criteria. I have an input sequence that contains characters A,T,G,C only. 

ALLOWED=("AA","AG","GC","GT","CA","CG","TT","TC ");
DISALLOWED=("AC","AT","GG","GA","CC","CT","TG","TA")

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using the above DISALLOWED regions when the program reads the input file it should chop(break) and continue. For the ALLOWED region it should not chop unless it finds a disallowed character. And also at the end of each line if the last character of each line and the first character of next line is in the ALLOWED region it should not chop. And also if the character N comes in between the sequence it should be chopped also. For Ex 

CTGTCAGCNNNCCGGTTTTCAAGNNGAGCACACACCAAAAATGCACCAAAGCTTNACATCCATACAAA

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For the above input sequence the output should be 

C
T 
GTCAGC 
NNN
C 
CG 
GTTTTCAAG 
NN
G 
AGCA 
CA 
CA 
C 
CAAAAA 
T 
GCA 
C 
CAAAGC 
TT 
N
A 
CA 
TC 
CA 
T 
A 
CAAA

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Edit: g0n - added code tags

2005-10-19 Retitled by g0n, as per Monastery guidelines
Original title: 'substring'

In reply to Extracting a substring according to some criteria by Benson

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