in reply to How do you match a stretch of at least N characters

Iterate over the possible positions in the longer string. Use XOR to get a string that contains zero bytes in positions where two strings are the same. Then just use tr to count the number of zeroes in substrings of length 10, report the positions if the number is 9 or 10. 
#!/usr/bin/perl
use warnings;
use strict;
use feature qw{ say };

my $small_str = 'AAATTGGTGTATATGAAAGACCTCGACGCTATTTAGAAAGAGAGAGCAATATT
+TCAAGAAT'
    . 'GCATGCGTCAATTTTACGCAGACTATCTTTCTAGGGTTAAATATACTGACAGTGTGCAGTGAC
+TCACAAAA'
    . 'GATGATTA';
my $reference_str = 'ACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGAC
+TGTGGTGG'
    . 'GGTCGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACGTCCATACT
+GAGAATCA'
    . 'TGTTAACATTAGTGGGTGCAGCGCACAAGCATGGCACATGTATACATATGTAACTAACCTGCA
+CAATGTGC'
    . 'ACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAAAAAAAAAAAAAAAAAACACATTAA
+AAAAAAAA'
    . 'AAAACAACAAAACAAAGCAAACATGGAAATGTTTGTTATTTTAATTGTTATGATGGTTTCATG
+GCTGTTTG'
    . 'CATGTGTCAAAACTCATCAAATTTGTGTACGTTAAATATGTGAAACTTATTGTATGCTGGTTA
+CACCTCAA'
    . 'TAAAGCTGTTAAATTTAAAAAAAAAAAAAAAAAAAAAAATCACCAATAGTTGCTGCTAGAAAT
+CCAGTGTC'
    . 'ACAAAAGGCCAAAGTTTATTGACAAATTGGTGTATATGAAAGACCTCGACGCTATTTAGAAAG
+AGAGAGCA'
    . 'ATATTTCAAGAATGCATGCGTCAATTTTACGCAGACTATCTTTCTAGGGTTAATCTAGCTGCA
+TCAGGATC'
    . 'ATATCGTCGGGTCTTTTTTCCGGCTCAGTCATCGCCCAAGCTGGCGCTATCTGGGCATCGGGG
+AGGAAGAA'
    . 'GCCCGTGCCTTTTCCCGCGAGGTTGAAGCGGCATGGAAAGAGTTTGCCGAGGATGACTGCTGC
+TGCATTGA'
    . 'CGTTGAGCGAAAACGCACGTTTACCATGATGATTCGGGAAGGTGTGGCCATGCACGCCTTTAA
+CGGTGAAC'
    . 'TGTTCGTTCAGGCCACCTGGGATACCAGTTCGTCGCGGCTTTTCCGGACACAGTTCCGGATGG
+TCAGCCCG'
    . 'AAGCGCATCAGCAACCCGAACAATACCGGCGACAGCCGGAACTGCCGTGCCGGTGTGCAGATT
+AATGACAG'
    . 'CGGTGCGGCGCTGGGATATTACGTCAGCGAGGACGGGTATCCTGGCTGGATGCCGCAGAAATG
+GACATGGA'
    . 'TACCCCGTGAGTTACCCGGCGGGCGCGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTG
+AAATTGTT'
    . 'ATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCT
+AATGAGTG'
    . 'AGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGC
+CAGCTGCA'
    . 'TTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTC
+GCTCACTG'
    . 'ACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATAC
+GGTTATCC'
    . 'ACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAAC
+CGTAAAAA'
    . 'GGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACG
+CTCAAGTC'
    . 'AGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCG
+TGCGCTCT'
    . 'CCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCG
+CTTTCTCA'
    . 'TAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCA
+CGAACCCC'
    . 'CCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGAC
+ACGACTTA'
    . 'TCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACA
+GAGTTCTT'
    . 'GAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAA
+GCCAGTTA'
    . 'CCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTT
+TTTTTGTT'
    . 'TGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACG
+GGGTCTGA'
    . 'CGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTT
+CACCTAGA'
    . 'TCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTG
+ACAGTTAC'
    . 'CAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCC
+TGACTCCC'
    . 'CGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACC
+GCGAGACC'
    . 'CACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAA
+GTGGTCCT'
    . 'GCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCG
+CCAGTTAA'
    . 'TAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTAT
+GGCTTCAT'
    . 'TCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGG
+TTAGCTCC'
    . 'TTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCA
+GCACTGCA'
    . 'TAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAA
+GTCATTCT'
    . 'GAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGC
+CACATAGC'
    . 'AGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTA
+CCGCTGTT'
    . 'GAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCAC
+CAGCGTTT'
    . 'CTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAAAAGGGCGACACGGAAATG
+TTGAATAC'
    . 'TCAT';

for my $start_pos (0 .. length($reference_str) - 11) {
    my $xor = $small_str ^ substr $reference_str, $start_pos, length($
+reference_str) - 1;
    for my $inner_pos (0 .. length($xor) - 10) {
        if (9 <= substr($xor, $inner_pos, 10) =~ tr/\0//) {

            say $start_pos + $inner_pos;
            say substr $small_str, $inner_pos, 10;
            say substr $reference_str, $start_pos + $inner_pos, 10;

        }
    }
}

[download]

TODO: Handle matches where the two strings don't fully overlap.

Update Probably like this? It wraps the longer string in characters that can never match, so some simple math is needed to get the original position back:

my $stretch = 10;
my $mismatches = 1;

substr $reference_str, 0, 0, 'x' x (length($small_str) - 1);
$reference_str .= 'x' x (length($small_str) - 1);

for my $start_pos (0 .. length($reference_str) - 1 - $stretch) {
    my $substr = substr $reference_str, $start_pos, length($small_str)
+ - 1;
    my $xor = $small_str ^ $substr;
    for my $inner_pos (0 .. length($xor) - $stretch) {
        if ($stretch - $mismatches <= substr($xor, $inner_pos, $stretc
+h) =~ tr/\0//) {
            my $match = substr $reference_str, $start_pos + $inner_pos
+, $stretch;
            next unless -1 == index $match, 'x';

            say $start_pos + $inner_pos + 1 - length $small_str;
            say substr $small_str, $inner_pos, $stretch;
            say $match;
        }
    }
}

[download]

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,

[download]

Replies are listed 'Best First'.
Re^2: How do you match a stretch of at least N characters
by Anonymous Monk on Sep 11, 2017 at 14:39 UTC
    Choroba, thank you very much for the code. I am bit confused, is the second part an addition to the previous one? Because - I think - I get only exact matches with the second part, or not?
[reply]
      No, it's a replacement. It reports 107 matches for me, 92 of them are exact.

      ($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,

      [download]
[reply]
[d/l]
        Aha, ok, I see, probably I just ran into the exact ones by chance... I know I am pushing my luck a bit, but since you have been so helpful and the code is yours, is there a way that I can see which of the 10-mers are consecutive and "paste" them into one larger match?
        AGCAATATTTCAAG
AGCAATATTTCAAG

GCAATATTTCAAGA
GCAATATTTCAAGA

        [download]

        For example, these 2 are basically the same, just going 1 position further.
        Hm, now that I am thinking it better, was the problem I asked for a question of finding the longest possible match with one mismatch allowed? Would that have been easier and I was wasting everyone's time here?
[reply]
[d/l]

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