20251125

99.scripts/trinity_utils/PerlLib/overlapping_nucs.ph

@@ -0,0 +1,61 @@
+#!/usr/local/bin/perl
+
+####
+sub nucs_in_common {
+    my ($e5, $e3, $g5, $g3) = @_;
+	
+
+    ($e5, $e3) = sort {$a<=>$b} ($e5, $e3);
+    ($g5, $g3) = sort {$a<=>$b} ($g5, $g3);
+
+	unless (&coordsets_overlap([$e5,$e3], [$g5, $g3])) {
+		return(0);
+	}
+	
+    my $length = abs ($e3 - $e5) + 1;
+    my $diff1 = ($e3 - $g3);
+    $diff1 = ($diff1 > 0) ? $diff1 : 0;
+    my $diff2 = ($g5 - $e5);
+    $diff2 = ($diff2 > 0) ? $diff2 : 0;
+    my $overlap_length = $length - $diff1 - $diff2;
+    return ($overlap_length);
+}
+
+####
+sub coordsets_overlap {
+	my ($coordset_A_aref, $coordset_B_aref) = @_;
+
+	my ($lend_A, $rend_A) = sort {$a<=>$b} @$coordset_A_aref;
+
+	my ($lend_B, $rend_B) = sort {$a<=>$b} @$coordset_B_aref;
+
+	if ($lend_A <= $rend_B && $rend_A >= $lend_B) {
+		## yes, overlap
+		return (1);
+	}
+	else {
+		return (0);
+	}
+}
+
+
+####
+sub coordset_A_encapsulates_B {
+	my ($coordset_A_aref, $coordset_B_aref) = @_;
+
+	my ($lend_A, $rend_A) = sort {$a<=>$b} @$coordset_A_aref;
+	
+	my ($lend_B, $rend_B) = sort {$a<=>$b} @$coordset_B_aref;
+	
+	if ($lend_A <= $lend_B && $rend_B <= $rend_A) {
+		return(1); # true
+	}
+	else {
+		return(0); # false;
+	}
+}
+
+
+
+1;
+