1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
|
#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\nusage: $0 RSEM.genes.results\n\n";
my $rsem_file = $ARGV[0] or die $usage;
main: {
my @entries;
open (my $fh, $rsem_file) or die $!;
my $header = <$fh>;
my $max_fpkm = 0;
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $len = $x[2];
my $fpkm = $x[6];
push (@entries, { len => $len,
fpkm => $fpkm,
});
if ($fpkm > $max_fpkm) {
$max_fpkm = $fpkm;
}
}
close $fh;
print join("\t", "min_fpkm", "cum_seq_len", "partial_sum_len", "N50_len", "num_entries") . "\n";
;
&N50(0, \@entries);
my $min_fpkm = 0.01;
while ($min_fpkm < $max_fpkm) {
@entries = grep { $_->{fpkm} >= $min_fpkm } @entries;
&N50($min_fpkm, \@entries);
$min_fpkm *= 2;
}
}
sub N50 {
my ($min_fpkm, $entries_aref) = @_;
my @entries = @$entries_aref;
@entries = reverse sort {$a->{len}<=>$b->{len}} @entries;
my $num_entries = scalar(@entries);
my $cum_seq_len = 0;
foreach my $entry (@entries) {
$cum_seq_len += $entry->{len};
}
my $half_cum_len = $cum_seq_len / 2;
my $n50_len = "NA";
my $partial_sum_len = 0;
foreach my $entry (@entries) {
my $len = $entry->{len};
$partial_sum_len += $len;
if ($partial_sum_len >= $half_cum_len) {
$n50_len = $len;
last;
}
}
print join("\t", $min_fpkm, int($cum_seq_len+0.5), int($partial_sum_len+0.5), $n50_len, $num_entries) . "\n";
return;
}
|
