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#!/usr/local/bin/perl -w
use lib '.';
use constant NUMTESTS => 4;
BEGIN {
eval { require Test; };
use Test;
plan tests => NUMTESTS;
}
# All tests must be run from the software directory;
# make sure we are getting the modules from here:
use strict;
use GO::Parser;
# ----- REQUIREMENTS -----
# ncbi_taxonomy roundtrips
# this test involves class properties
# ------------------------
if (1) {
my $f = './t/data/sample.ncbi_taxonomy';
my $f2 = cvt($f,'ncbi_taxonomy','obo');
# some taxon terms contain {} - test that escaping of these works
open(F,$f2) || die;
my $matched;
while (<F>) {
# ID 21 has a fake {...} entry
if (/\\\{test\\\}/) {
$matched=1;
last;
}
}
ok($matched);
my $parser = new GO::Parser;
$parser->parse($f2);
my $obo = $parser->handler->stag;
ok($obo->get('header/synonymtypedef'));
ok($obo->get('term/synonym/@/synonym_type'));
my @terms = $obo->get_term;
my ($t) = grep {$_->sget_id eq 'NCBITaxon:21'} @terms;
# some taxon terms contain {} - test that escaping of these works
print $t->get_name,"\n";
ok($t->get_name eq 'Phenylobacterium immobile {test}');
}
exit 0;
sub cvt {
my $f = shift;
my ($from, $to) = @_;
print "$f from:$from to:$to\n";
my $parser = new GO::Parser ({format=>$from,
handler=>$to});
my $outf = "$f.$to";
unlink $outf if -f $outf;
$parser->handler->file($outf);
$parser->parse($f);
return $outf;
}
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