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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: PrimarySeq.t,v 1.14 2002/03/08 20:18:32 jason 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 => 23;
}
use Bio::PrimarySeq;
use Bio::Location::Simple;
use Bio::Location::Fuzzy;
use Bio::Location::Split;
ok(1);
my $seq = Bio::PrimarySeq->new('-seq' =>'TTGGTGGCGTCAACT',
'-display_id' => 'new-id',
'-alphabet' => 'dna',
'-accession_number' => 'X677667',
'-desc' =>'Sample Bio::Seq object');
ok defined $seq;
ok $seq->isa('Bio::PrimarySeqI');
ok $seq->accession_number(), 'X677667';
ok $seq->seq(), 'TTGGTGGCGTCAACT';
ok $seq->display_id(), 'new-id';
ok $seq->alphabet(), 'dna';
ok $seq->is_circular(), undef;
ok $seq->is_circular(1);
my $location = new Bio::Location::Simple('-start' => 2, '-end' => 5,
'-strand' => -1);
ok ($seq->subseq($location), 'ACCA');
my $splitlocation = new Bio::Location::Split();
$splitlocation->add_sub_Location( new Bio::Location::Simple('-start' => 1,
'-end' => 4,
'-strand' => 1));
$splitlocation->add_sub_Location( new Bio::Location::Simple('-start' => 7,
'-end' => 12,
'-strand' => -1));
ok( $seq->subseq($splitlocation), 'TTGGTGACGC');
my $fuzzy = new Bio::Location::Fuzzy(-start => '<3',
-end => '8',
-strand => 1);
ok( $seq->subseq($fuzzy), 'GGTGGC');
my $trunc = $seq->trunc(1,4);
ok defined $trunc;
ok $trunc->seq(), 'TTGG', "Expecting TTGG. Got ".$trunc->seq();
$trunc = $seq->trunc($splitlocation);
ok( defined $trunc);
ok( $trunc->seq(), 'TTGGTGACGC');
$trunc = $seq->trunc($fuzzy);
ok( defined $trunc);
ok( $trunc->seq(), 'GGTGGC');
my $rev = $seq->revcom();
ok defined $rev;
ok $rev->seq(), 'AGTTGACGCCACCAA', 'rev faile was ' . $rev->seq();
#
# Translate
#
my $aa = $seq->translate();
ok $aa->seq, 'LVAST', "Translation: ". $aa->seq;
$seq->seq('TTGGTGGCGTCAACTTAA');
$aa = $seq->translate(undef, undef, undef, undef, 1);
# tests for non-Methionin initiator codon (AGT) coding for M
ok $aa->seq, 'MVAST', "Translation: ". $aa->seq;
# test for character '?' in the sequence string
ok $seq->seq('TTGGTGGCG?CAACT'), 'TTGGTGGCG?CAACT';
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