20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,119 @@
+package main;
+our $SEE = 0;
+
+
+package CDNA::Overlap_assembler;
+
+use strict;
+
+sub new {
+    my $packagename = shift;
+    my $self = {
+	node_list => []
+	};
+    bless ($self, $packagename);
+    return ($self);
+}
+
+sub add_cDNA {
+    my $self = shift;
+    my ($cdna_acc, $end5, $end3) = @_;
+    my ($cdna_start, $cdna_stop) = sort {$a<=>$b} ($end5, $end3);
+    my $node = Cdna_node->new($cdna_acc, $cdna_start, $cdna_stop);
+    push (@{$self->{node_list}}, $node);
+}
+
+
+####
+sub build_clusters {
+    my $self = shift;
+    my $node_list_aref = $self->{node_list};
+    @{$node_list_aref} = sort {$a->{lend}<=>$b->{lend}} @{$node_list_aref}; #sort by lend coord.
+    ## set indices
+    for (my $i = 0; $i <= $#{$node_list_aref}; $i++) {
+	$node_list_aref->[$i]->{myIndex} = $i;
+    }
+    
+    my @clusters;
+    my $first_node = $node_list_aref->[0];
+    my $start_pos = 0;
+    my ($exp_left, $exp_right) = ($first_node->{lend}, $first_node->{rend});
+    print $first_node->{acc} . " ($exp_left, $exp_right)\n" if $SEE;
+    for (my $i = 1; $i <= $#{$node_list_aref}; $i++) {
+	my $curr_node = $node_list_aref->[$i];
+	my ($lend, $rend) = ($curr_node->{lend}, $curr_node->{rend});
+	print $curr_node->{acc} . " ($lend, $rend)\n" if $SEE;
+	if ($exp_left <= $rend && $exp_right >= $lend) { #overlap
+	    $exp_left = &min($exp_left, $lend);
+	    $exp_right = &max($exp_right, $rend);
+	    print "overlap. New expanded coords: ($exp_left, $exp_right)\n" if $SEE;
+	} else {
+	    print "No overlap; Creating cluster: " if $SEE;
+	    my @cluster;
+	    for (my $j=$start_pos; $j < $i; $j++) {
+		my $acc = $node_list_aref->[$j]->{acc};
+		push (@cluster, $acc);
+		print "$acc, " if $SEE;
+	    }
+	    push (@clusters, [@cluster]);
+	    $start_pos = $i;
+	    ($exp_left, $exp_right) = ($lend, $rend);
+	    print "\nResetting expanded coords: ($lend, $rend)\n" if $SEE;
+	}
+    }
+
+    print "# Adding final cluster.\n" if $SEE;
+    if ($start_pos != $#{$node_list_aref}) {
+	print "final cluster: " if $SEE;
+	my @cluster;
+	for (my $j = $start_pos; $j <= $#{$node_list_aref}; $j++) {
+	   my $acc = $node_list_aref->[$j]->{acc};
+	   print "$acc, " if $SEE;
+	   push (@cluster, $acc);
+       }
+	push (@clusters, [@cluster]);
+	print "\n" if $SEE;
+    } else {
+	my $acc = $node_list_aref->[$start_pos]->{acc};
+	push (@clusters, [$acc]);
+	print "adding final $acc.\n" if $SEE;
+    }
+    return (@clusters);
+}
+
+sub min {
+    my (@x) = @_;
+    @x = sort {$a<=>$b} @x;
+    my $min = shift @x;
+    return ($min);
+}
+
+sub max {
+    my @x = @_;
+    @x = sort {$a<=>$b} @x;
+    my $max = pop @x;
+    return ($max);
+}
+
+#################################################################
+package Cdna_node;
+use strict;
+
+sub new {
+    my $packagename = shift;
+    my ($acc, $lend, $rend) = @_;
+    my $self = { acc=>$acc,
+		 lend=>$lend,
+		 rend=>$rend,
+		 myIndex=>undef(),
+		 overlapping_indices=>[]
+		 };
+    bless ($self, $packagename);
+    return ($self);
+}
+
+1; #EOM
+
+
+
+