/usr/bin/go-show-paths-to-root is in libgo-perl 0.15-5.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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 | #!/usr/bin/perl
# POD docs at end of file
use strict;
use Getopt::Long;
use FileHandle;
use GO::Parser;
use Data::Stag;
$|=1;
my $opt = {};
GetOptions($opt,
"help|h",
"format|p=s",
"err|e=s",
"id=s@",
"names",
"use_cache",
);
if ($opt->{help}) {
system("perldoc $0");
exit;
}
my $errf = $opt->{err};
my $errhandler = Data::Stag->getformathandler('xml');
if ($errf) {
$errhandler->file($errf);
}
else {
$errhandler->fh(\*STDERR);
}
my @ids = @{$opt->{id} || []};
if (!@ids) {
print STDERR "specify id list with -id ID option\n";
exit 1;
}
my @files = GO::Parser->new->normalize_files(@ARGV);
while (my $fn = shift @files) {
my $fn = shift;
my %h = %$opt;
my $fmt;
if ($fn =~ /\.obo/) {
$fmt = 'obo_text';
}
if ($fmt && !$h{format}) {
$h{format} = $fmt;
}
$h{handler} = 'obj';
my $parser = new GO::Parser(%h);
$parser->litemode(1);
$parser->errhandler($errhandler);
$parser->parse($fn);
my $g = $parser->handler->graph;
foreach my $id (@ids) {
my $t = $g->get_term($id);
if (!$t) {
next;
}
printf "%s %s\n", $id, $t->name;
my $paths = $g->paths_to_top($id) || [];
foreach my $path (@$paths) {
printf " PATH: %s\n",
$path->to_text($opt->{names} ? () : ('acc'));
}
}
}
$errhandler->finish;
exit 0;
__END__
=head1 NAME
go-show-paths-to-root.pl - shows all possible paths from a term to the top
=head1 SYNOPSIS
go-show-paths-to-root.pl -id GO:0008021 ontology/gene_ontology.obo
go-show-paths-to-root.pl -names -id GO:0008021 ontology/gene_ontology.obo
=head1 DESCRIPTION
traverses DAG showing all paths (terms and intervening relationships)
to the root
This script is purely file based; it needs to parse the ontology each time
Subsequent parses can be speeded up using the use_cache option
If you wish to use the GO MySQL db, see the script
go-db-show-paths-to-root.pl in the go-db-perl distribution
=head1 ARGUMENTS
=head3 -e ERRFILE
writes parse errors in XML - defaults to STDERR
(there should be no parse errors in well formed files)
=head3 -p FORMAT
determines which parser to use; if left unspecified, will make a guess
based on file suffix. See below for formats
=head2 -use_cache
If this switch is specified, then caching mode is turned on.
With caching mode, the first time you parse a file, then an additional
file will be exported in a special format that is fast to parse. This
file will have the same filename as the original file, except it will
have the ".cache" suffix.
The next time you parse the file, this program will automatically
check for the existence of the ".cache" file. If it exists, and is
more recent than the file you specified, this is parsed instead. If it
does not exist, it is rebuilt.
=head2 DOCUMENTATION
L<http://www.godatabase.org/dev>
=cut
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