I don't really know what you mean by "non-reciprocal edges", but if I get it right, then you want want to find all the connected components in a directed graph, so try this:
use strict;
use warnings;
use Data::Dump qw( pp );
sub find_parts {
my %graph = %{ shift() };
my %seen;
my @parts;
my $i = 0;
my $helper;
$helper = sub {
my $start = shift;
return if $seen{$start}++;
push @{ $parts[$i] }, $start;
$helper->($_) for @{ $graph{$start} };
};
for ( keys %graph ) {
$helper->($_);
$i = $#parts + 1;
}
undef $helper;
return @parts;
}
my %graph;
while (<DATA>) {
my ( $src, $dst ) = split;
push @{ $graph{$src} }, $dst;
}
pp \%graph;
pp find_parts( \%graph );
__DATA__
Contig1 Contig2
Contig1 Contig3
Contig2 Contig1
Contig2 Contig3
Contig3 Contig1
Contig3 Contig2
Contig3 Contig4
Contig4 Contig3
Contig4 Contig5
Contig6 Contig7
Contig7 Contig6
Contig8 Contig9
Contig9 Contig10
Contig10 Contig8
Contig10 Contig11
Contig11 Contig10
foo bar
bar foo
quux quux
I haven't tested all the edge cases, but this will give you the idea.
Hope that helps.
update: LanX is right, my code above does not work for the case he has shown. Something like this would have been better to implement: Tarjan's strongly connected components algorithm
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