1# -*-Perl-*- Test Harness script for Bioperl 2# $Id$ 3 4use strict; 5 6BEGIN { 7 use Bio::Root::Test; 8 9 test_begin(-tests => 30); 10 11 use_ok('Bio::Seq::LargePrimarySeq'); 12 use_ok('Bio::Seq::LargeSeq'); 13 use_ok('Bio::Location::Simple'); 14 use_ok('Bio::Location::Fuzzy'); 15 use_ok('Bio::Location::Split'); 16 use_ok('Bio::SeqIO'); 17} 18 19my $pseq = Bio::Seq::LargePrimarySeq->new(); 20ok $pseq; 21$pseq->add_sequence_as_string('ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAAT'); 22$pseq->add_sequence_as_string('GTTTGGGGTTAAACCCCTTTGGGGGGT'); 23 24is $pseq->display_id('hello'), 'hello'; 25 26is $pseq->seq, 'ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGGGGGT' , "Sequence is " . $pseq->seq; 27 28is $pseq->subseq(3,7), 'GGGGT', "Subseq is ".$pseq->subseq(3,7); 29my $location = Bio::Location::Simple->new(-start => 4, -end => 8, 30 -strand => 1); 31is($pseq->subseq($location), 'GGGTG'); 32 33my $splitlocation = Bio::Location::Split->new(); 34 35$splitlocation->add_sub_Location( Bio::Location::Simple->new('-start' => 1, 36 '-end' => 15, 37 '-strand' => 1)); 38 39$splitlocation->add_sub_Location( Bio::Location::Simple->new('-start' => 21, 40 '-end' => 27, 41 '-strand' => -1)); 42 43is( $pseq->subseq($splitlocation), 'ATGGGGTGGGGTGAACCCCCAA'); 44 45my $fuzzy = Bio::Location::Fuzzy->new(-start => '<10', 46 -end => '18', 47 -strand => 1); 48 49is( $pseq->subseq($fuzzy), 'GGTGAAACC'); 50 51 52is($pseq->trunc(8,15)->seq, 'GGGGTGAA', 53 'trunc seq was ' . $pseq->trunc(8,15)->seq); 54 55 56is $pseq->alphabet('dna'), 'dna'; # so translate will not complain 57is $pseq->translate()->seq, 'MGWGETLWGWGKCLGLNPFGG'; 58 59 60my $seq = Bio::Seq::LargeSeq->new(-primaryseq => $pseq ); 61 62is $seq->display_id('hello'), 'hello'; 63 64is $seq->seq, 'ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGGGGGT' , "Sequence is " . $seq->seq; 65 66# test SeqIO::fasta (allows LargeSeqI; bug 2490) 67 68SKIP: { 69 eval {require IO::String}; 70 skip "SeqIO output for LargeSeq requires IO::String", 2 if $@; 71 my $str; 72 my $strobj = IO::String->new($str); 73 my $out = Bio::SeqIO->new(-fh => $strobj, -format => 'fasta'); 74 ok($out->write_seq($seq)); 75 like($str, qr/>hello\nATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGG\nGGGT/, 76 'output via Bio::SeqIO::fasta'); 77} 78 79is $seq->subseq(3,7), 'GGGGT', "Subseq is ".$seq->subseq(3,7); 80is ($seq->trunc(8,15)->seq, 'GGGGTGAA', 81 'trunc seq was ' . $seq->trunc(8,15)->seq); 82 83is $seq->alphabet('dna'), 'dna'; # so translate will not complain 84is $seq->translate()->seq, 'MGWGETLWGWGKCLGLNPFGG'; 85 86$seq = Bio::Seq::LargeSeq->new( -display_id => 'hello'); 87$seq->seq('ATGGGGTGGGGT'); 88is $seq->display_id, 'hello'; 89 90is $seq->seq, 'ATGGGGTGGGGT' , "Sequence is " . $seq->seq; 91 92is $seq->subseq(3,7), 'GGGGT', "Subseq is ".$seq->subseq(3,7); 93is ($seq->trunc(8,12)->seq, 'GGGGT', 94 'trunc seq was ' . $seq->trunc(8,12)->seq); 95 96is $seq->alphabet('dna'), 'dna'; # so translate will not complain 97is $seq->translate()->seq, 'MGWG'; 98