src/hg/utils/automation/n50.pl 1.2

Index: src/hg/utils/automation/n50.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/n50.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/utils/automation/n50.pl	7 Aug 2009 17:50:43 -0000	1.1
+++ src/hg/utils/automation/n50.pl	7 Aug 2009 18:16:48 -0000	1.2
@@ -1,75 +1,75 @@
 #!/usr/bin/env perl
 # n50.pl - calculate N50 values for a two column file
 
 
 # $Id$
 
 use strict;
 use warnings;
 
 my $argc = scalar(@ARGV);
 
 if ($argc < 1) {
     printf STDERR "n50.pl - calculate N50 values from a two column file\n";
     printf STDERR "usage:\n\tn50.pl <contigs.sizes> [other.sizes]\n";
     printf STDERR "\twhere <contigs.sizes> is a two column file:\n";
     printf STDERR "\tcontigName size\n";
     exit 255;
 }
 
 while (my $sizeFile = shift) {
     my $sizeCount = 0;
 
     my %sizes;	# key is contigName, value is size
 
     if ($sizeFile eq "stdin") {
 	printf STDERR "#\treading: stdin\n";
 	while (my $line = <>) {
 	    next if ($line =~ m/^\s*#/);
 	    ++$sizeCount;
 	    chomp ($line);
 	    my ($name, $size) = split('\s+', $line);
 	    $sizes{$name} = $size;
 	}
     } else {
 	printf STDERR "#\treading: $sizeFile\n";
 	open (FH, "<$sizeFile") or die "can not read $sizeFile";
 	while (my $line = <FH>) {
 	    next if ($line =~ m/^\s*#/);
 	    ++$sizeCount;
 	    chomp ($line);
 	    my ($name, $size) = split('\s+', $line);
 	    $sizes{$name} = $size;
 	}
 	close (FH);
     }
 
     my $totalSize = 0;
     foreach my $key (keys %sizes) {
 	$totalSize += $sizes{$key}
     }
     my $n50Size = $totalSize / 2;
 
-    printf STDERR "#\tcontig count: %d, total size: %d, N50 size: %d\n",
+    printf STDERR "#\tcontig count: %d, total size: %d, one half size: %d\n",
 	    $sizeCount, $totalSize, $n50Size;
 
     my $prevContig = "";
     my $prevSize = 0;
 
     $totalSize = 0;
     my $contigCount =0;
     foreach my $key (sort { $sizes{$b} <=> $sizes{$a} } keys %sizes) {
 	++$contigCount;
 	$totalSize += $sizes{$key};
 	if ($totalSize > $n50Size) {
 	    printf "# cumulative\tN50 count\tcontig\tcontig size\n";
 	    printf "%d\t%d\t%s\t%d\n",
 		$totalSize-$sizes{$key},$contigCount-1,$prevContig, $prevSize;
 	    printf "%d one half size\n", $n50Size;
 	    printf "%d\t%d\t%s\t%d\n", $totalSize, $contigCount, $key, $sizes{$key};
 	    last;
 	}
 	$prevContig = $key;
 	$prevSize = $sizes{$key};
     }
 }