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
|
#!/usr/bin/env perl
use strict;
use warnings;
my $usage = <<__EOUSAGE__;
###############################################
#
# Usage: $0 matrix.txt new_feature_id_mapping.txt
#
# The 'new_feature_id_mapping.txt' file has the format:
#
# current_identifier <tab> new_identifier
# ....
#
#
# Only those entries with new names listed will be updated, the rest stay unchanged.
#
#
#################################################
__EOUSAGE__
;
my $matrix_file = $ARGV[0] or die $usage;
my $new_feature_mappings = $ARGV[1] or die $usage;
main: {
my %new_ids;
{
open (my $fh, $new_feature_mappings) or die $!;
while (<$fh>) {
chomp;
my ($old_name, $new_name) = split(/\t/);
$new_ids{$old_name} = $new_name;
}
close $fh;
}
open (my $fh, $matrix_file) or die $!;
while (<$fh>) {
unless(/\w/) {
print;
next;
}
chomp;
my @ids = split(/\t/);
$ids[0] =~ s/\|.*$//;
if (my $new_id = $new_ids{$ids[0]}) {
$ids[0] = $new_id;
}
if (scalar(@ids) > 1 && (my $new_id = $new_ids{$ids[1]})) {
$ids[1] = $new_id;
}
print join("\t", @ids) . "\n";
}
exit(0);
}
|
