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
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
|
#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
#############################################################################################
usage: $0 [--top_ranks <int>] pw1 pw2 ...
##############################################################################################
#
# --top_ranks <int> restrict to number of top ranked entries per pairwise condition.
#
# --minFC <float> minimum fold change in expression
#
##############################################################################################
__EOUSAGE__
;
my $help_flag;
my $top_ranks = -1;
my $minFC = 0;
&GetOptions ( 'h' => \$help_flag,
'top_ranks=i' => \$top_ranks,
'minFC=f' => \$minFC,
);
my $minLogFC = 0;
if ($minFC) {
$minLogFC = log($minFC)/log(2);
}
my @summaries = @ARGV or die $usage;
unless (scalar @summaries > 1) {
die $usage;
}
main: {
if ($top_ranks > 0) {
print STDERR "NOTE: only $top_ranks top ranks from each will be reported.\n\n";
}
my %gene_samples_to_methods;
my %gene_samples_to_ranks;
foreach my $summary (@summaries) {
my %pw_counter;
open (my $fh, $summary) or die $!;
while (<$fh>) {
chomp;
my ($acc, $sampleA, $sampleB, $exprA, $exprB, $logFC, $pval) = split(/\t/);
if (abs($logFC) < $minLogFC) { next; }
my $feature_sample_key = join("$;", $acc, sort ($sampleA, $sampleB));
my $sample_key = join("$;", sort($sampleA, $sampleB));
$pw_counter{$sample_key}++;
#if ($top_ranks > 0 && $pw_counter{$sample_key} > $top_ranks) { next; }
#print STDERR "$pw_counter{$sample_key}\n";
push (@{$gene_samples_to_methods{$feature_sample_key}}, $summary);
$gene_samples_to_ranks{$feature_sample_key}->{$summary} = $pw_counter{$sample_key};
}
close $fh;
}
## output
foreach my $feature_samples (keys %gene_samples_to_methods) {
my @methods = sort (@{$gene_samples_to_methods{$feature_samples}});
my @rankings;
my $report_entry = ($top_ranks > 0) ? 0 : 1;
foreach my $method (@methods) {
my $rank = $gene_samples_to_ranks{$feature_samples}->{$method};
push (@rankings, $rank);
if ($top_ranks > 0 && $rank <= $top_ranks) {
$report_entry = 1;
}
}
if ($report_entry) {
my ($feature, $sampleA, $sampleB) = split(/$;/, $feature_samples);
print join("\t", $feature, $sampleA, $sampleB, join(",", @methods), join(",", @rankings) ) . "\n";
}
}
exit(0);
}
|
