#! perl -slw use strict; use Data::Dump qw[ pp ]; my $k = 15; my %repo = ( "readA" => "AAACATGAAAAGAAATGATGAAACAGA", "readB" => "AAATCATGAAACAGAGCCTCATCTCCC ", ); my @order = ( "readB_1","readA_2"); #my $k = 25; #my %repo = ( # "readA" => "GCTGAGGCAGGAGAATTGCTTGAACCTGGGAGGCA", # "readB" => "TACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAAC", # "readC" => "GCTGAGGCAGGAGAATTGCTTGAACTTAGGGGATG", # "readD" => "TACTCGGGAGGCTGAGGCAGGAGAATTGCTTGAAC", #); #my @order = ( "readA_1", "readB_2", "readC_1", "readD_2"); sub muster { local $^W; my( $bits ) = @_; my $muster = ''; for my $p ( 0 .. length( $bits->[0] )-1 ) { my %uniq; ++$uniq{ substr $bits->[ $_ ], $p, 1 } for 0 .. $#$bits; if( keys %uniq > 1 ) { $muster .= '(' . join( ',', keys %uniq ) . ')'; } else { $muster .= each %uniq; } } return $muster; } my( @heads, @bodys, @tails ); while( @order ) { my( $s1, $p1, $s2, $p2 ) = map split( '_', shift @order ), 1 .. 2; ( $s1, $s2 ) = ( $s2, $s1 ) if $p1 > $p2; push @heads, substr $repo{ $s2 }, 0, length( $repo{ $s2 } ) - $k; push @bodys, substr $repo{ $s2 }, -$k; push @tails, substr $repo{ $s1 }, $k; push @bodys, substr $repo{ $s1 }, 0, $k; } my $head = muster( \@heads ); my $body = muster( \@bodys ); my $tail = muster( \@tails ); print $head, $body, $tail; __END__ TACTC(A,G)GGAGGAGAATTGCTTGAACCTGGGAGGCA(T,C)T(A,G)GG(A,G)G(A,G)(T,C)(A,G) TACTC(A,G)GGAGGCTGAGGCAGGAGAATTGCTTGAAC(T,C)T(A,G)GG(A,G)G(A,G)(T,C)(A,G) AAACATGAAAAGAAAT(C,G)ATGAAACAGAGCCTCATCTCCC AAACATGAAAAGAAAT(G,C)ATGAAACAGAGCCTCATCTCCC