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
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
|
#!/usr/bin/perl -w
#
# freqdiff - print frequency difference between two inputs
#
# <@LICENSE>
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to you under the Apache License, Version 2.0
# (the "License"); you may not use this file except in compliance with
# the License. You may obtain a copy of the License at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# </@LICENSE>
our ($opt_a, $opt_b, $opt_c, $opt_d, $opt_h, $opt_p, $opt_r, $opt_l);
use Getopt::Std;
getopts("abcdhprl:");
my $prog = $0;
$prog =~ s@.*/@@;
sub usage {
my $status = shift;
my $out = $status ? STDERR : STDOUT;
print $out <<EOF;
usage: $prog [options] [first input] [second input]
$prog [options] [first input] [second input] [scores file]
-a show all elements (only used for -d)
-b show both count and percentage
-c remove comments from inputs
-d print delta of frequencies (second - first)
-h print this help
-p print percentage of frequencies ((first / (first + second)) * 100.0)
-r use relative frequencies (account for size of inputs, useful for -p)
-l N only read first N lines
default is -d if input line counts are within 1% of each other and -p otherwise
EOF
exit($status);
}
usage(0) if $opt_h;
usage(1) unless $#ARGV > 0;
my @line;
my $type;
my %one = read_argv(0);
my %two = read_argv(1);
$opt_d = 1 if (!$opt_p && (abs($line[0] - $line[1]) / $line[1]) < 0.01);
$opt_d = 1 if ($type == 3);
$opt_a = 1 if ($type == 4);
my %score;
if ($#ARGV > 1) {
open(FILE, $ARGV[2]) || die "open failed: $ARGV[2]";
while (<FILE>) {
chomp;
s/#.*//;
my @field = split;
if ($#field >= 2 && $field[0] eq "score") {
$score{$field[1]} = $field[2];
}
}
close(FILE);
}
my @all = (keys %one);
foreach my $elem (keys %two) {
if (! defined($one{$elem})) {
push(@all, $elem);
}
}
my %out;
foreach my $elem (@all) {
my $one = 0;
my $two = 0;
if ($type == 3) {
$one = 1.0;
$two = 1.0;
}
if (exists($one{$elem})) {
$one = $one{$elem};
delete $one{$elem};
}
if (exists($two{$elem})) {
$two = $two{$elem};
delete $two{$elem};
}
if ($opt_d) {
$out{$elem} = $two - $one;
}
else {
$count{$elem} = $two + $one if $opt_b;
$out{$elem} = $one / ($one + $two) * 100.0;
}
}
foreach my $elem (sort { $out{$b} <=> $out{$a} || ((defined %count) && ($count{$b} <=> $count{$a})) || $a cmp $b } keys %out) {
my $name = $elem;
if (%score) {
if (exists($score{$elem})) {
$name = "$score{$elem}\t$name";
}
else {
$name = "1.0\t$name";
}
}
if ($type == 3) {
printf "%.3f\t%s\n", $out{$elem}, $name;
}
elsif ($opt_d) {
print "$out{$elem}\t$name\n" if ($out{$elem} || $opt_a);
}
else {
if ($opt_b) {
printf "%.2f\t%d\t%s\n", $out{$elem}, $count{$elem}, $name;
}
else {
printf "%.2f\t%s\n", $out{$elem}, $name;
}
}
}
sub read_argv {
my ($input) = @_;
my %freq;
my $last = 0;
open(FILE, $ARGV[$input]) || die "open failed: $ARGV[$input]";
my $line = 0;
while(<FILE>) {
if ($opt_c) {
s/#.*//;
next unless /\S/;
}
next if (/^OVERALL/); # hit-frequencies header line
$line++;
next if ($opt_l && $line > $opt_l);
$last = $type;
# "sort | uniq -c" format
if (/^\s*(-?\d+|-?\d+\.\d+)\s+(.*)/) {
$type = 1;
$freq{$2} = $1;
}
# "mass-check" format
elsif (/^[Y.]\s+-?\d+\s+\S+\s+(\S+)/) {
my $test_str = $1;
$type = 2;
foreach my $r (split(/,/, $test_str)) {
my $hits = 1;
# Support compacted RULE(hitcount) format
if ($r =~ s/\((\d+)\)$//) {
$hits = $1;
}
$freq{$r} += $hits;
}
}
# "scores" format
elsif (/^score\s+(\S+)\s+(-?[\d.]+)/) {
$type = 3;
$freq{$1} = $2;
}
# line number is frequency
else {
$type = 4;
chomp;
$freq{$_} = $line;
}
if ($last && $last != $type) {
die "$prog: inconsistent format in $ARGV[$input] (format $last then format $type)\n";
}
}
close(FILE);
foreach my $key (keys %freq) {
if ($type == 4) {
$freq{$key} = $line - $freq{$key} + 1;
}
if ($opt_r) {
$freq{$key} /= $line;
}
}
$line[$input] = $line;
return %freq;
}
|
