# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 28);
use_ok('Bio::SeqIO');
use_ok('Bio::SeqFeature::Gene::Transcript');
use_ok('Bio::SeqFeature::Gene::UTR');
use_ok('Bio::SeqFeature::Gene::Exon');
use_ok('Bio::SeqFeature::Gene::Poly_A_site');
use_ok('Bio::SeqFeature::Gene::GeneStructure');
use_ok('Bio::Location::Fuzzy');
}
my ( $seqio, $geneseq, $gene, $transcript, $poly_A_site1, $poly_A_site2,
$fiveprimeUTR, $exon);
# tests for Bio::SeqFeature::Gene::* objects
# using information from acc: AB077698 as a guide
ok $seqio = Bio::SeqIO->new(
-format => 'genbank',
-file => test_input_file('AB077698.gb'),
);
ok $geneseq = $seqio->next_seq();
ok $gene = Bio::SeqFeature::Gene::GeneStructure->new(
-primary => 'gene',
-start => 1,
-end => 2701,
-strand => 1,
);
ok $transcript = Bio::SeqFeature::Gene::Transcript->new(
-primary => 'CDS',
-start => 80,
-end => 1144,
-tag => {
'gene' => "CHCR",
'note' => "Cys3His CCG1-Required Encoded on BAC clone RP5-842K24 (AL050310) The human CHCR (Cys3His CCG1-Required) protein is highly related to EXP/MBNL (Y13829, NM_021038, AF401998) and MBLL (NM_005757,AF061261), which together comprise the human Muscleblind family",
'codon_start' => 1,
'protein_id' => 'BAB85648.1',
}
);
ok $poly_A_site1 = Bio::SeqFeature::Gene::Poly_A_site->new(
-primary => 'polyA_site',
-start => 2660,
-end => 2660,
-tag => {
'note' => "Encoded on BAC clone RP5-842K24 (AL050310); PolyA_site#2 used by CHCR EST clone DKFZp434G2222 (AL133625)"
}
);
ok $poly_A_site2 = Bio::SeqFeature::Gene::Poly_A_site->new(
-primary => 'polyA_site',
-start => 1606,
-end => 1606,
-tag => {
'note' => "Encoded on BAC clone RP5-842K24 (AL050310); PolyA_site#1 used by CHCR EST clone PLACE1010202 (AK002178)",
}
);
ok $fiveprimeUTR = Bio::SeqFeature::Gene::UTR->new(-primary => "utr5prime");
ok $fiveprimeUTR->location(
Bio::Location::Fuzzy->new(
-start => "<1",
-end => 79,
)
);
ok my $threeprimeUTR = Bio::SeqFeature::Gene::UTR->new(
-primary => "utr3prime",
-start => 1145,
-end => 2659,
);
# Did a quick est2genome against genomic DNA (this is on Chr X) to
# get the gene structure by hand since it is not in the file
# --Jason
ok $exon = Bio::SeqFeature::Gene::Exon->new(
-primary => 'exon',
-start => 80,
-end => 177,
);
ok $geneseq->add_SeqFeature($exon);
ok $geneseq->add_SeqFeature($fiveprimeUTR);
ok $geneseq->add_SeqFeature($threeprimeUTR);
ok $geneseq->add_SeqFeature($poly_A_site1);
ok $geneseq->add_SeqFeature($poly_A_site2);
ok $transcript->add_utr($fiveprimeUTR, 'utr5prime');
ok $transcript->add_utr($threeprimeUTR, 'utr3prime');
ok $transcript->add_exon($exon);
# API only supports a single poly-A site per transcript at this point
$transcript->poly_A_site($poly_A_site2);
$geneseq->add_SeqFeature($transcript);
$gene->add_transcript($transcript);
$geneseq->add_SeqFeature($gene);
my ($t) = $gene->transcripts(); # get 1st transcript
ok(defined $t);
is($t->mrna->length, 1693, 'mRNA spliced length');
is($gene->utrs, 2, 'has 2 UTRs');