20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,62 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+my $usage = "usage: $0 file.frag_coords (LEND|REND)\n\n";
+
+my $file = $ARGV[0] or die $usage;
+my $end = $ARGV[1] or die $usage;
+
+unless ($end eq "LEND" || $end eq "REND") {
+    die $usage;
+}
+
+main: {
+
+    my @histogram;
+    my $curr_scaffold = "";
+    
+    open (my $fh, $file) or die $usage;
+    while (<$fh>) {
+        chomp;
+        my ($scaff, $read, $lend, $rend) = split(/\t/);
+        if ($curr_scaffold ne $scaff) {
+            &write_wig($curr_scaffold, \@histogram) if @histogram;
+        
+            # re-init
+            $curr_scaffold = $scaff;
+            @histogram = ();
+        }
+        
+        my $pos = ($end eq "LEND") ? $lend : $rend;
+        
+        
+        $histogram[$pos]++;
+    }
+    close $fh;
+    
+    if (@histogram) {
+        &write_wig($curr_scaffold, \@histogram);
+    }
+
+    exit(0);
+}
+
+####
+sub write_wig {
+    my ($scaffold, $histogram_aref) = @_;
+
+    print "variableStep chrom=$scaffold\n";
+
+    for (my $i = 1; $i <= $#$histogram_aref; $i++) {
+        my $val = $histogram_aref->[$i];
+        if (defined $val) {
+            print join("\t", $i, $val) . "\n";
+        }
+    }
+
+    return;
+}
+
+