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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 49,
-requires_modules => [qw(XML::SAX XML::SAX::Writer)]);
use_ok('Bio::SeqIO::tigrxml');
}
my $verbose = test_debug();
my $ast = Bio::SeqIO->new(-format => 'tigrxml' ,
-verbose => $verbose,
-file => test_input_file('test.tigrxml'));
isa_ok($ast, 'Bio::SeqIO');
$ast->verbose($verbose);
ok my $as = $ast->next_seq();
is($as->display_id, 'chr9');
my $first = 1;
for my $f ( sort { $a->start * $a->strand <=> $b->start * $b->strand } $as->get_SeqFeatures ) {
ok($f);
my ($name);
for my $tag ( qw(Parent ID) ) {
if( $f->has_tag($tag) ) {
($name) = $f->get_tag_values($tag);
last;
}
}
if( $name eq '162.t00500' || $name eq '162.m02638' ) {
if( $f->primary_tag eq 'gene' ) {
is($f->start, 185408);
is($f->end, 187155);
# warn($f->gff_string, "\n");
} elsif( $f->primary_tag eq 'mRNA' ) {
is($f->start, 185408); # the values list for COORD are start/end of CDS not whole transcript
is($f->end, 187155);
is($f->strand, 1);
} elsif( $f->primary_tag eq "five_prime_UTR" ) {
my ($id) = $f->get_tag_values('ID');
if( $id =~ /UTR1$/ ) {
is($f->start, 185408);
is($f->end, 185433);
} elsif( $id =~ /UTR2$/ ) {
is($f->start, 185487);
is($f->end, 185793);
} else {
ok(0, 'expected only two UTRS');
}
} elsif( $f->primary_tag eq "three_prime_UTR" ) {
is($f->start, 187042);
is($f->end, 187155);
} elsif( $f->primary_tag eq 'CDS' ) {
is($f->start, 185794);
is($f->end, 187041);
}
} elsif ( $name eq '162.t00448' || $name eq '162.m02967' ) {
if( $f->primary_tag eq 'gene' ) {
is($f->start, 59343);
is($f->end, 61061);
} elsif( $f->primary_tag eq 'mRNA' ) {
is($f->start, 59343); # the values list for COORD are start/end of CDS not whole transcript
is($f->end, 61061);
is($f->strand, -1);
} elsif( $f->primary_tag eq "five_prime_UTR" ) {
my ($id) = $f->get_tag_values('ID');
is($f->start, 60834);
is($f->end, 61061);
is($f->strand, -1);
} elsif( $f->primary_tag eq "three_prime_UTR" ) {
is($f->start, 59343);
is($f->end, 59632);
is($f->strand, -1);
} elsif( $f->primary_tag eq 'CDS' ) {
if( $first ) {
is($f->start, 60801);
is($f->end, 60833);
is($f->strand, -1);
$first = 0;
}
}
} else {
ok(0, "unexpected name '$name'\n");
}
}
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