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|
#-*-Perl-*-
## Bioperl Test Harness Script for Modules
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan test => 32;
}
use Bio::Seq;
use Bio::Tools::GFF;
use Bio::SeqFeatureI;
use Bio::SeqFeature::Generic;
my $feat = new Bio::SeqFeature::Generic( -start => 10, -end => 100,
-strand => -1, -primary => 'repeat',
-source => 'repeatmasker',
-score => 1000,
-tag => {
new => 1,
author => 'someone',
sillytag => 'this is silly!;breakfast' } );
ok($feat);
my $gff1out = Bio::Tools::GFF->new(-gff_version => 1, -file => ">out1.gff");
ok($gff1out);
my $gff2out = Bio::Tools::GFF->new(-gff_version => 2, -file => ">out2.gff");
ok($gff2out);
$gff1out->write_feature($feat);
$gff2out->write_feature($feat);
$gff1out->close();
$gff2out->close();
my $gff1in = Bio::Tools::GFF->new(-gff_version => 1, -file => "out1.gff");
ok($gff1in);
my $gff2in = Bio::Tools::GFF->new(-gff_version => 2, -file => "out2.gff");
ok($gff2in);
my $feat1 = $gff1in->next_feature();
ok($feat1);
ok($feat1->start, $feat->start);
ok($feat1->end, $feat->end);
ok($feat1->primary_tag, $feat->primary_tag);
ok($feat1->score, $feat->score);
my $feat2 = $gff2in->next_feature();
ok($feat2);
ok($feat2->start, $feat->start);
ok($feat2->end, $feat->end);
ok($feat2->primary_tag, $feat->primary_tag);
ok($feat2->score, $feat->score);
ok(($feat2->each_tag_value('sillytag'))[0], 'this is silly!;breakfast');
#test sequence-region parsing
$gff2in = Bio::Tools::GFF->new(-gff_version => 2, -file => Bio::Root::IO->catfile("t","data","hg16_chroms.gff"));
ok($gff2in->next_feature(),undef);
my $seq = $gff2in->next_segment;
ok($seq->display_id, 'chr1');
ok($seq->end, 246127941);
ok($seq->start, 1);
# GFF3
eval { require IO::String };
unless( $@ ) {
my $str = IO::String->new;
my $gffout = new Bio::Tools::GFF(-fh => $str, -gff_version => 3);
my $feat_test = new Bio::SeqFeature::Generic
(-primary_tag => 'tag',
-source_tag => 'exon',
-seq_id => 'testseq',
-score => undef,
-start => 10,
-end => 120,
-strand => 1,
-tag => {
'bungle' => 'jungle;mumble',
'lion' => 'snake=tree'
});
$feat_test->add_tag_value('giant_squid', 'lakeshore manor');
$gffout->write_feature($feat_test);
seek($str,0,0);
my $in = new Bio::Tools::GFF(-fh => $str,
-gff_version => 3);
my $f_recon = $in->next_feature;
ok($f_recon->primary_tag, $feat_test->primary_tag);
ok($f_recon->source_tag, $feat_test->source_tag);
ok($f_recon->score, $feat_test->score);
ok($f_recon->start, $feat_test->start);
ok($f_recon->end, $feat_test->end);
ok($f_recon->strand, $feat_test->strand);
for my $tag ( $feat_test->get_all_tags ) {
ok($f_recon->has_tag($tag));
if( $f_recon->has_tag($tag) ) {
my @v = $feat_test->get_tag_values($tag);
my @g = $f_recon->get_tag_values($tag);
while( @v && @g ) {
ok(shift @v, shift @g);
}
}
}
} else {
for ( 17..28 ) {
skip('cannot verify GFF3 writing tests without IO::String installed',1);
}
}
END {
unlink("out1.gff", "out2.gff");
}
|
