[Bioperl-l] Help with String::Approx
tembe at bioanalysis.org
Mon Mar 14 12:19:59 EST 2005
Thanks for the advice to use String::Approx.
I installed String::Approx and it seems to be functional. Just as a
check, I am trying to run different utilities such as adist, aindex etc.
by following the examples on CPAN's string::approx page and can't seem
to run aslice utility. For the following code, adist and aindex seem to
work fine. But aslice outputs something unexpected.
$F = "xxxx";
$S = "zzzxxyxyyy";
print "Edit = ", adist($F, $S), "\n";
$index = aindex($F, $S);
print "Matches at ", $index, "\n";
($index, $size) = aslice($F, $S);
print "Matches at ", $index, "\tSize is ", $size, "\n";
($index, $size, $d) = aslice($F, $S);
print "Matches at ", $index, "\tSize is ", $size, "Distance is ", $d, "\n";
Edit = 1
Matches at 3
Matches at ARRAY(0x9cc9d98) Size is
Matches at ARRAY(0x9ddfbc0) Size is Distance is
Any help to fix this and to use Approx utility for:
1. Extracting the approximate match from $S
2. At least finding the length of the match and correct index in $S
will be appreciated.
Andrew Walsh wrote:
> The following cpan module may be of interest:
> Waibhav Tembe wrote:
>> I was wondering if there is any Perl implementation for
>> "k-differences" string matching algorithm using dynamic programming.
>> More precisely, given two string s1 and s2, the program finds an
>> alignment, if one exists, that has less than or equal to k (a
>> parameter) no. of differences. The differences include mismatches and
>> Any pointers will be welcome.
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
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