Re: Recovering Substrings to String with Gap

it's because you always search the substring from the beginning instead of from the point after the last match.

my $after = 0;
foreach my $sbstr ( @$array ) {
       my $pos = index $str, $sbstr, $after;
       substr ($nstring, $pos, length ($sbstr)) = $sbstr;
       $after=$pos+length($sbstr);
}
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Re^2: Recovering Substrings to String with Gap by monkfan (Curate) on Apr 16, 2005 at 11:14 UTC
No it wont' do, cause it will "over append" those overlapping substrings (@arr2 and @arr3) which gives: `GATTACGNNNNNNNNNCGTGTAANNNNTTACGAG NNNTACGAGTNNNGCTCGTGNNNNNNNGTGGCGC` [download] Instead of OP (already) correct answers. Regards, Edward	[reply] [d/l]
Re^3: Recovering Substrings to String with Gap by salva (Canon) on Apr 16, 2005 at 12:03 UTC
oops, you are right, I had supposed that the strings didn't overlap... but if the substrings are sorted by their position on the original string, it's easy to solve, just make $after=$pos+1 or: `my $pos=0; foreach my $sbstr ( @$array ) { $pos = index $str, $sbstr, $pos; substr ($nstring, $pos, length ($sbstr)) = $sbstr; $pos++ }` [download] and if they are not sorted, well, then you can use some hash to remember the last $pos for a given $sbstr and start searching after that... `my %after; foreach my $sbstr ( @$array ) { my $pos = index $str, $sbstr, $after{$sbstr}\|\|0; substr ($nstring, $pos, length ($sbstr)) = $sbstr; $after{$sbstr}=$pos+1; }` [download]	[reply] [d/l] [select]