20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,202 @@
+package WigParser;
+
+use strict;
+use warnings;
+use Carp;
+
+####
+sub new {
+    my $packagename = shift;
+    my ($wig_file) = @_;
+
+    unless ($wig_file) {
+        confess "Error, need wig_filename as parameter to constructor";
+    }
+
+    my $self = { wig_file => $wig_file,
+                 wig_file_fh => undef,
+                 contig_to_seek_pos_href => {},
+             };
+
+    bless ($self, $packagename);
+    
+    $self->_init_wig_info();
+
+
+    return($self);
+}
+
+####
+sub _init_wig_info {
+    my $self = shift;
+
+    my $wig_file = $self->{wig_file};
+    
+
+    open (my $fh, $wig_file) or die "Error, cannot open file $wig_file";
+    $self->{wig_file_fh} = $fh;
+    
+    while (<$fh>) {
+        if (/chrom=(\S+)/) {
+			my $scaff = $1;
+            my $filepos = tell($fh);
+            $self->{contig_to_seek_pos_href}->{$scaff} = $filepos;
+        }
+    }
+    
+
+    return;
+}
+
+####
+sub get_contig_list {
+    my $self = shift;
+    
+    my @contigs = keys %{$self->{contig_to_seek_pos_href}};
+
+    return(@contigs);
+}
+
+####
+sub get_wig_array {
+    my $self = shift;
+    my ($contig, $extended_flag) = @_;
+    
+    
+    my $seekpos = $self->{contig_to_seek_pos_href}->{$contig};
+    
+    unless (defined $seekpos) {
+        confess "Error, cannot find seek position entry for contig: $contig";
+    }
+
+    my $fh = $self->{wig_file_fh};
+
+    seek($fh, $seekpos, 0); 
+
+    #print STDERR "-retrieving wig array for $contig at pos: $seekpos\n";
+    
+    my @wig_array;
+
+    while (<$fh>) {
+        
+        if (/chrom=/) { last; }
+        
+        chomp;
+        my ($pos, $val, @rest) = split(/\s+/);
+        if ($pos > 1e12) {
+            confess "Error, position $pos is out of range of max contig position value set at 1e12";
+        }
+        if ($extended_flag) {
+            $wig_array[$pos] = [$val, @rest];
+        }
+        else {
+            $wig_array[$pos] = $val;
+        }
+        
+    }
+    
+    # fill in missing entries
+    foreach my $val (@wig_array) {
+        if (! defined ($val)) {
+            $val = 0;
+        }
+    }
+
+
+    return(@wig_array);
+}
+
+
+
+#####################################################################
+## Static method that uses LOTS of memory (original implementation)
+
+sub parse_wig {
+	my ($wig_file) = @_;
+
+	my %scaff_to_coverage;
+    
+	print STDERR "-retrieving max positions per scaffold\n";
+	my %max_vals_for_scaffs = &_parse_max_scaff_lengths($wig_file);
+	
+	print STDERR "-preallocating memory for coverage\n";
+	## preallocate arrays for coverage
+
+	my $sum_pos = 0;
+	foreach my $scaff (keys %max_vals_for_scaffs) {
+		my $max_val = $max_vals_for_scaffs{$scaff};
+
+		my @cov_vals = ();
+		$#cov_vals = $max_val;
+		
+		for my $index (0..$max_val) {
+			$cov_vals[$index] = int(0);
+		}
+		$scaff_to_coverage{$scaff} = \@cov_vals;
+		
+		$sum_pos += $max_val;
+	
+	}
+
+	print STDERR "- $sum_pos bases represented\n";
+
+	print STDERR "-populating coverage data into memory.\n";
+	
+	my $scaff = undef;
+
+	open (my $fh, $wig_file) or die "Error, cannot open file $wig_file";
+	while (<$fh>) {
+		if (/^track/) { next; };
+		if (/chrom=(\S+)/) {
+			$scaff = $1;
+			next;
+		}
+		chomp;
+		my ($pos, $val) = split(/\s+/);
+		$scaff_to_coverage{$scaff}->[$pos] = $val;
+		
+	}
+	
+	close $fh;
+
+	return(%scaff_to_coverage);
+}
+
+
+
+### Private
+
+sub _parse_max_scaff_lengths {
+	my ($wig_file) = @_;
+
+	my %scaff_to_max_vals;
+	
+	my $scaff = "";
+
+
+	my $counter = 0;
+	open (my $fh, $wig_file) or die "Error, cannot open file $wig_file";
+	while (<$fh>) {
+		if (/^track/) { next; };
+		if (/chrom=(\S+)/) {
+			$scaff = $1;
+			next;
+		}
+		chomp;
+		my ($pos, $val) = split(/\s+/);
+		$scaff_to_max_vals{$scaff} = $pos;
+		
+		#print "scaff: $scaff\t$pos=> $val\n";
+		
+		$counter++;
+
+		#if ($counter > 100000) { last; }
+	}
+	
+	close $fh;
+
+	return(%scaff_to_max_vals);
+}
+
+1; #EOM
+