Dear Sirs,
I have the following problem.
I am trying to put the bracket in a string given the set of its substrings.
Those bracketed region is "bounded" by the given substrings.
Like this, given input "String" and it's "substrings"
String
1.CCCATCTGTCCTTATTTGCTG
2.ACCCATCTGTCCTTGGCCAT
3.CCACCAGCACCTGTC
4.CCCAACACCTGCTGCCT
5.CTGGGTATGGGT
6.AGGAACTTGCCTGTACCACAGGAAG
Substrings:
1. ATCTG ATTTG
2. CCATC
3. CCACC CCAGC GCAAC
4. CCAAC ACACC
5. GTATG TGGGT
6. CAGGA AGGAA
The desired answer are:
1. CCC[ATCTG]TCCTT[ATTTG]CTG
2. AC[CCATC]TGTCCTTGGCCAT
3. [CCACCAGCACC]TGTC *
4. C[CCAACACC]TGCTGCCT *
5. CTGG[GTATGGGT] **
6. AGGAACTTGCCTGTACCA[CAGGAA]G **
Please note that in example 3 and 4 the substrings are "overlapping".
Pay attention also to for example 5 and 6, there exist substrings that occur
twice. So the answer for example 5 and 6 are NOT
5. C[TGGGTATGGGT] ----this is wrong
6. [AGGAA]CTTGCCTGTACCA[CAGGAA]G ----this is wrong
Since they do not follow the order from the given substrings (array -- see my
code).
Below is my code. It only work for example 1 and 2.
How can I approach this problem so that it can handle all those cases?
__BEGIN__
#!/usr/bin/perl -w
use strict;
my $s1 ='CCCATCTGTCCTTATTTGCTG'; my @a1 = qw(ATCTG ATTTG);
my $s2 ='ACCCATCTGTCCTTGGCCAT'; my @a2 = qw(CCATC);
my $s3 ='CCACCAGCACCTGTC'; my @a3 = qw(CCACC CCAGC GCACC);
my $s4 ='CCCAACACCTGCTGCCT'; my @a4 = qw(CCAAC ACACC);
my $s5 ='CTGGGTATGGGT'; my @a5 = qw(GTATG TGGGT);
my $s6 = 'AGGAACTTGCCTGTACCACAGGAAG'; my @a6 = qw( CAGGA AGGAA );
#These two work fine.
put_bracket($s1,[EMAIL PROTECTED]);
put_bracket($s2,[EMAIL PROTECTED]);
#But these the rest don't work
put_bracket($s3,[EMAIL PROTECTED]);
put_bracket($s4,[EMAIL PROTECTED]);
put_bracket($s5,[EMAIL PROTECTED]);
put_bracket($s6,[EMAIL PROTECTED]);
sub put_bracket
{
my ($str,$ar) = @_;
my $bstr;
my $slen = length $ar->[0];
foreach my $subs ( @$ar )
{
my $idx = index($str,$subs);
my $bgn = $idx;
my $end = $idx+$slen+1;
substr($str,$bgn,0,"[");
substr($str,$end,0,"]");
}
print "$str\n";
return ;
__END__
Really hope to hear from you again.
---
Regards,
Edward WIJAYA
SINGAPORE
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