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package main;
our $CLUSTERPATH;
package SingleLinkageClusterer;
## package not to be instantiated. Just provides a namespace.
## Input: Array containing array-refs of pairs:
## @_ = ( [1,2], [2,3], [6,7], [7,8], ...)
## Output: Array of all clusters as array-refs.
## return ([1,2,3] , [6,7,8], ...)
use strict;
sub build_clusters {
my @pairs = @_;
my $pairfile = "$$.pairs";
#must do mapping because cluster program doesn't like word chars, just ints.
my %map_id_to_feat;
my %map_feat_to_id;
my $id = 1;
open (PAIRLIST, ">$pairfile") or die "Can't write $pairfile to /tmp";
foreach my $pair (@pairs) {
my ($a, $b) = @$pair;
unless ($map_feat_to_id{$a}) {
$map_feat_to_id{$a} = $id;
$map_id_to_feat{$id} = $a;
$id++;
}
unless ($map_feat_to_id{$b}) {
$map_feat_to_id{$b} = $id;
$map_id_to_feat{$id} = $b;
$id++;
}
print PAIRLIST "$map_feat_to_id{$a} $map_feat_to_id{$b}\n";
}
close PAIRLIST;
my $clusterfile = "$$.clusters";
my $cluster_prog = "slclust";
if ($CLUSTERPATH) {
$cluster_prog = $CLUSTERPATH;
}
system "touch $clusterfile";
unless (-w $clusterfile) { die "Can't write $clusterfile";}
my $cmd = "$cluster_prog < $pairfile > $clusterfile";
my $ret = system ($cmd);
if ($ret) {
die "ERROR: Couldn't run cluster properly via path: $cluster_prog.\ncmd: $cmd";
}
my @clusters;
open (CLUSTERS, $clusterfile);
while (my $line = <CLUSTERS>) {
my @elements;
while ($line =~ /(\d+)\s?/g) {
push (@elements, $map_id_to_feat{$1});
}
if (@elements) {
push (@clusters, [@elements]);
}
}
close CLUSTERS;
## clean up
unlink ($pairfile, $clusterfile);
return (@clusters);
}
1;
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