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|
# -*-Perl-*-
## Bioperl Test Harness Script for Modules
##
# CVS Version
# $Id: SeqFeature.t,v 1.20 2001/10/22 08:22:58 heikki Exp $
# 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( $@ ) {
use lib 't';
}
use Test;
plan tests => 37;
}
use Bio::Seq;
use Bio::SeqFeature::Generic;
use Bio::SeqFeature::FeaturePair;
use Bio::SeqFeature::SimilarityPair;
use Bio::Tools::Blast;
use Bio::SeqFeature::Computation;
ok(1);
# predeclare variables for strict
my ($feat,$str,$feat2,$pair,$comp_obj1,$comp_obj2,@sft);
$feat = new Bio::SeqFeature::Generic ( -start => 40,
-end => 80,
-strand => 1,
-primary => 'exon',
-source => 'internal',
-tag => {
silly => 20,
new => 1
}
);
ok $feat->start, 40;
ok $feat->end, 80;
ok $feat->primary_tag, 'exon';
ok $feat->source_tag, 'internal';
$str = $feat->gff_string() || ""; # placate -w
# we need to figure out the correct mapping of this stuff
# soon
#if( $str ne "SEQ\tinternal\texon\t40\t80\t1\t.\t." ) {
# print "not ok 3\n";
#} else {
# print "ok 3\n";
#}
ok(1);
$pair = new Bio::SeqFeature::FeaturePair();
ok defined $pair;
$feat2 = new Bio::SeqFeature::Generic ( -start => 400,
-end => 440,
-strand => 1,
-primary => 'other',
-source => 'program_a',
-tag => {
silly => 20,
new => 1
}
);
ok defined $feat2;
$pair->feature1($feat);
$pair->feature2($feat2);
ok $pair->feature1, $feat;
ok $pair->feature2, $feat2;
ok $pair->start, 40;
ok $pair->end, 80;
ok $pair->primary_tag, 'exon';
ok $pair->source_tag, 'internal';
ok $pair->hstart, 400;
ok $pair->hend, 440;
ok $pair->hprimary_tag, 'other' ;
ok $pair->hsource_tag, 'program_a';
$pair->invert;
ok $pair->end, 440;
# Test attaching a SeqFeature::Generic to a Bio::Seq
{
# Make the parent sequence object
my $seq = Bio::Seq->new(
'-seq' => 'aaaaggggtttt',
'-display_id' => 'test',
'-alphabet' => 'dna',
);
# Make a SeqFeature
my $sf1 = Bio::SeqFeature::Generic->new(
'-start' => 4,
'-end' => 9,
'-strand' => 1,
);
# Add the SeqFeature to the parent
ok ($seq->add_SeqFeature($sf1));
# Test that it gives the correct sequence
my $sf_seq1 = $sf1->seq->seq;
ok $sf_seq1, 'aggggt';
ok $sf1->end,9;
ok $sf1->start,4;
# Make a second seqfeature on the opposite strand
my $sf2 = Bio::SeqFeature::Generic->new(
'-start' => 4,
'-end' => 9,
'-strand' => -1,
);
# This time add the PrimarySeq to the seqfeature
# before adding it to the parent
ok ($sf2->attach_seq($seq->primary_seq));
$seq->add_SeqFeature($sf2);
# Test again that we have the correct sequence
my $sf_seq2 = $sf2->seq->seq;
ok $sf_seq2, 'acccct';
}
#Do some tests for computation.pm
ok defined ( $comp_obj1 = Bio::SeqFeature::Computation->new('-start' => 1,
'-end' => 10) );
ok ( $comp_obj1->computation_id(332) );
ok ( $comp_obj1->add_score_value('P', 33) );
{
$comp_obj2 = Bio::SeqFeature::Computation->new('-start' => 2,
'-end' => 10);
ok ($comp_obj1->add_sub_SeqFeature($comp_obj2, 'exon') );
ok (@sft = $comp_obj1->all_sub_SeqFeature_types() );
ok ($sft[0], 'exon');
}
# some tests for bug #947
my $sfeat = new Bio::SeqFeature::Generic(-primary => 'test');
$sfeat->add_sub_SeqFeature(new Bio::SeqFeature::Generic(-start => 2,
-end => 4,
-primary => 'sub1'),
'EXPAND');
$sfeat->add_sub_SeqFeature(new Bio::SeqFeature::Generic(-start => 6,
-end => 8,
-primary => 'sub2'),
'EXPAND');
ok($sfeat->start, 2);
ok($sfeat->end, 8);
# some tests to see if we can set a feature to start at 0
$sfeat = new Bio::SeqFeature::Generic(-start => 0, -end => 0 );
ok(defined $sfeat->start);
ok($sfeat->start,0);
ok(defined $sfeat->end);
ok($sfeat->end,0);
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