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Id: 94529
Status: new
Priority: 0/
Queue: String-Approx

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Owner: Nobody in particular
Requestors: q.zhao [...] uq.edu.au
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Subject: bug in String::Approx 'adist'?
Date: Tue, 8 Apr 2014 05:20:56 +0000
To: "bug-String-Approx [...] rt.cpan.org" <bug-String-Approx [...] rt.cpan.org>
From: Qiongyi Zhao <q.zhao [...] uq.edu.au>
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Dear developer(s) of the "String-Approx" module, I found a strange result when I tried to get the edit distance between two strings. My testing perl script is listed below: ########################## a simple perl script to show the bug ########################## #!/usr/bin/perl -w use strict; use warnings; use String::Approx 'adist'; my $seq1="ATCTGACACATGTTTACTTTGTAGCTTAGCCCCAACAAACACACACTXAGGAGAGTCTACATTCXCTGCTTGAATCCTAGTTACGACAGCAACAGGTCTG"; my $seq2="ATCTGACACATGTTTACTTTGTAGCTTAGCCCCAACAAACACACACTCAGGAGAGTCTACATTCACTGCTTGAATCCTAGTTACGACAGCAACAGGTCTG"; my $distance = adist($seq1, $seq2); #fuzzy match print STDERR "$distance\n"; ########################## a simple perl script to show the bug ########################## The output is "1" from this simple perl script. It is obvious to see that two letters are different between these two strings (marked as below), but how come the distance is only 1? Is it a bug for String::Approx 'adist'? my $seq1="ATCTGACACATGTTTACTTTGTAGCTTAGCCCCAACAAACACACACT[X]AGGAGAGTCTACATTC[X]CTGCTTGAATCCTAGTTACGACAGCAACAGGTCTG"; my $seq2="ATCTGACACATGTTTACTTTGTAGCTTAGCCCCAACAAACACACACT[C]AGGAGAGTCTACATTC[A]CTGCTTGAATCCTAGTTACGACAGCAACAGGTCTG"; Hope you could fix this bug. Thanks very much for your attention and for this nice module. # info of my testing environment Distribution name and version: String-Approx-3.27 Perl version: perl 5, version 14, subversion 2 (v5.14.2) built for x86_64-linux-thread-multi Operating System vendor and version: Linux cluster.qbi.uq.edu.au 2.6.32-220.13.1.el6.x86_64 #1 SMP Tue Apr 17 23:56:34 BST 2012 x86_64 x86_64 x86_64 GNU/Linux Best regards, Qiongyi Qiongyi Zhao| PhD |Bioinformatics Queensland Brain Institute | The University of Queensland Tel: +61 7 33466429| Mobile: 04 01219121 | Email: q.zhao@uq.edu.au<mailto:s.lee12@uq.edu.au>


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