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Re: Fast Identification Of String Difference

by AnomalousMonk (Abbot)
on Jan 17, 2011 at 03:31 UTC ( #882593=note: print w/ replies, xml ) Need Help??


in reply to Fast Identification Of String Difference

The 'classic' Perlish approach to this type of problem involves bitwise string boolean operations. The string  $diff generated by the bitwise-xor of characters in original sequence strings can be used to produce masks that can then be used to extract the differing sub-string sequences from the original strings.

use warnings; use strict; my $s1 = 'ACTGGACGTATGCA'; my $s2 = 'AGTG-ACGC-CGCA'; my $diff = $s1 ^ $s2; my @dpos; push @dpos, [ $-[1], $+[1] - $-[1] ] while $diff =~ m{ ([^\x00]+) }xmsg; print qq{diff at offset $_->[0], length $_->[1] \n} for @dpos; (my $mask = $diff) =~ tr{\x00}{\xff}c; $s1 &= $mask; $s2 &= $mask; my $differences = qr{ [^\x00]+ }xms; @dpos = (); while ($s1 =~ m{ ($differences) }xmsg) { # this code produces same result # my @diff_data = ($1); # $s2 =~ m{ ($differences) }xmsg; # push @diff_data, $1, $-[1]; # push @dpos, \@diff_data; push @dpos, [ $1, do { $s2 =~ m{ ($differences) }xmsg && $1, $-[1] } ] ; } print qq{@$_ \n} for @dpos;

Output:

diff at offset 1, length 1 diff at offset 4, length 1 diff at offset 8, length 3 C G 1 G - 4 TAT C-C 8

See @- and @+ in perlvar, also Bitwise Or and Exclusive Or and Bitwise And in perlop.

BrowserUk is very good on this general topic.

Update: Added better code example, doc links. And thanks to ELISHEVA.

Update: Fixed @- link above. What was I thinking?


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Re^2: Fast Identification Of String Difference
by johngg (Abbot) on Jan 17, 2011 at 10:52 UTC

    Using a look-ahead with pos can save having to do the sums.

    knoppix@Microknoppix:~$ perl -E ' > $s1 = q{ACTGGACGTATGCA}; > $s2 = q{AGTG-ACGC-CGCA}; > $m = $s1 ^ $s2; > push @pos, pos( $m ) while $m =~ m{(?=([^\x00]))}g; > $m =~ tr{[\x01-\xfe]}{\xff}; > $c1 = $s1 & $m; > @p1 = $c1 =~ m{([^\x00])}g; > $c2 = $s2 & $m; > @p2 = $c2 =~ m{([^\x00])}g; > printf qq{%-2s%-2s%6d\n}, $p1[ $_ ], $p2[ $_ ], $pos[ $_ ] > for 0 .. $#pos;' C G 1 G - 4 T C 8 A - 9 T C 10 knoppix@Microknoppix:~$

    I hope this is of interest.

    Cheers,

    JohnGG

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