—#!/usr/bin/perl
# $Id: ancestors.pl,v 1.4 2003/11/26 18:46:14 sherlock Exp $
# License information (the MIT license)
# Copyright (c) 2003 Gavin Sherlock; Stanford University
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, merge,
# publish, distribute, sublicense, and/or sell copies of the Software,
# and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
# The above copyright notice and this permission notice shall be
# included in all copies or substantial portions of the Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
use
strict;
use
diagnostics;
use
warnings;
my
(
$goid
,
$ontologyFile
) =
@ARGV
;
&Usage
(
"You must provide a goid"
)
if
(!
$goid
);
&Usage
(
"You must provide an ontology file"
)
if
(!
$ontologyFile
);
&Usage
(
"Your ontology file does not exist"
)
if
(!-e
$ontologyFile
);
my
$ontology
= GO::OntologyProvider::OntologyParser->new(
ontologyFile
=>
$ontologyFile
);
my
$node
=
$ontology
->nodeFromId(
$goid
);
my
@pathsToRoot
=
$node
->pathsToRoot;
foreach
my
$path
(
@pathsToRoot
){
for
(
my
$i
= 0;
$i
< @{
$path
};
$i
++){
" "
x
$i
,
$path
->[
$i
]->goid,
" "
,
$path
->[
$i
]->term,
"\n"
;
}
" "
x @{
$path
} ,
$node
->goid,
" "
,
$node
->term,
"\n"
;
"\n"
;
}
sub
Usage{
my
$message
=
shift
;
$message
,
".\n\n"
;
"Usage :
ancestors.pl <goid> <ontology_file>\n\n";
exit
;
}
=pod
=head1 NAME
ancestors.pl - prints paths from root to a GO node
=head1 SYNOPSIS
ancestors.pl simply takes as input a GOID, and an ontology file, and prints out
the all the paths from that GO node to the root of the ontology, e.g:
>ancestors.pl GO:0008346 ../t/process.ontology
GO:0003673 Gene_Ontology
GO:0008150 biological_process
GO:0007610 behavior
GO:0030537 larval behavior
GO:0008345 larval locomotory behavior
GO:0008346 larval walking behavior
GO:0003673 Gene_Ontology
GO:0008150 biological_process
GO:0007610 behavior
GO:0007626 locomotory behavior
GO:0008345 larval locomotory behavior
GO:0008346 larval walking behavior
=head1 AUTHORS
Gavin Sherlock, sherlock@genome.stanford.edu
=cut