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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 30);
use_ok('Bio::Seq::LargePrimarySeq');
use_ok('Bio::Seq::LargeSeq');
use_ok('Bio::Location::Simple');
use_ok('Bio::Location::Fuzzy');
use_ok('Bio::Location::Split');
use_ok('Bio::SeqIO');
}
my $pseq = Bio::Seq::LargePrimarySeq->new();
ok $pseq;
$pseq->add_sequence_as_string('ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAAT');
$pseq->add_sequence_as_string('GTTTGGGGTTAAACCCCTTTGGGGGGT');
is $pseq->display_id('hello'), 'hello';
is $pseq->seq, 'ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGGGGGT' , "Sequence is " . $pseq->seq;
is $pseq->subseq(3,7), 'GGGGT', "Subseq is ".$pseq->subseq(3,7);
my $location = Bio::Location::Simple->new(-start => 4, -end => 8,
-strand => 1);
is($pseq->subseq($location), 'GGGTG');
my $splitlocation = Bio::Location::Split->new();
$splitlocation->add_sub_Location( Bio::Location::Simple->new('-start' => 1,
'-end' => 15,
'-strand' => 1));
$splitlocation->add_sub_Location( Bio::Location::Simple->new('-start' => 21,
'-end' => 27,
'-strand' => -1));
is( $pseq->subseq($splitlocation), 'ATGGGGTGGGGTGAACCCCCAA');
my $fuzzy = Bio::Location::Fuzzy->new(-start => '<10',
-end => '18',
-strand => 1);
is( $pseq->subseq($fuzzy), 'GGTGAAACC');
is($pseq->trunc(8,15)->seq, 'GGGGTGAA',
'trunc seq was ' . $pseq->trunc(8,15)->seq);
is $pseq->alphabet('dna'), 'dna'; # so translate will not complain
is $pseq->translate()->seq, 'MGWGETLWGWGKCLGLNPFGG';
my $seq = Bio::Seq::LargeSeq->new(-primaryseq => $pseq );
is $seq->display_id('hello'), 'hello';
is $seq->seq, 'ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGGGGGT' , "Sequence is " . $seq->seq;
# test SeqIO::fasta (allows LargeSeqI; bug 2490)
SKIP: {
eval {require IO::String};
skip "SeqIO output for LargeSeq requires IO::String", 2 if $@;
my $str;
my $strobj = IO::String->new($str);
my $out = Bio::SeqIO->new(-fh => $strobj, -format => 'fasta');
ok($out->write_seq($seq));
like($str, qr/>hello\nATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGG\nGGGT/,
'output via Bio::SeqIO::fasta');
}
is $seq->subseq(3,7), 'GGGGT', "Subseq is ".$seq->subseq(3,7);
is ($seq->trunc(8,15)->seq, 'GGGGTGAA',
'trunc seq was ' . $seq->trunc(8,15)->seq);
is $seq->alphabet('dna'), 'dna'; # so translate will not complain
is $seq->translate()->seq, 'MGWGETLWGWGKCLGLNPFGG';
$seq = Bio::Seq::LargeSeq->new( -display_id => 'hello');
$seq->seq('ATGGGGTGGGGT');
is $seq->display_id, 'hello';
is $seq->seq, 'ATGGGGTGGGGT' , "Sequence is " . $seq->seq;
is $seq->subseq(3,7), 'GGGGT', "Subseq is ".$seq->subseq(3,7);
is ($seq->trunc(8,12)->seq, 'GGGGT',
'trunc seq was ' . $seq->trunc(8,12)->seq);
is $seq->alphabet('dna'), 'dna'; # so translate will not complain
is $seq->translate()->seq, 'MGWG';
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