1# -*-Perl-*- Test Harness script for Bioperl 2# $Id$ 3 4use strict; 5 6BEGIN { 7 use Bio::Root::Test; 8 9 test_begin(-tests => 14); 10 11 use_ok('Bio::Align::Utilities', qw(:all)); 12 use_ok('Bio::SimpleAlign'); 13 use_ok('Bio::PrimarySeq'); 14 use_ok('Bio::LocatableSeq'); 15 use_ok('Bio::AlignIO'); 16} 17 18my $DEBUG = test_debug(); 19 20my $aa_align = Bio::SimpleAlign->new(); 21$aa_align->add_seq(Bio::LocatableSeq->new(-id => "n1", -seq => "MLIDVG-MLVLR")); 22$aa_align->add_seq(Bio::LocatableSeq->new(-id => "n2", -seq => "MLIDVRTPLALR")); 23$aa_align->add_seq(Bio::LocatableSeq->new(-id => "n3", -seq => "MLI-VR-SLALR")); 24 25my %dnaseqs = (); 26$dnaseqs{'n1'} = Bio::PrimarySeq->new(-id => "n1dna", -seq => 'atgctgatagacgtaggcatgctagtactgaga'); 27$dnaseqs{'n2'} = Bio::PrimarySeq->new(-id => "n2dna", -seq => 'atgctgatcgacgtacgcaccccgctagcactcaga'); 28$dnaseqs{'n3'} = Bio::PrimarySeq->new(-id => "n3dna", -seq => 'atgttgattgtacgctcgcttgcacttaga'); 29my $dna_aln; 30 31ok( $dna_aln = &aa_to_dna_aln($aa_align, \%dnaseqs)); 32if( $DEBUG ) { 33 Bio::AlignIO->new(-format=>'clustalw')->write_aln($dna_aln); 34} 35 36is $dna_aln->length, 36; 37is $dna_aln->num_residues, 99; 38is $dna_aln->num_sequences, 3; 39is $dna_aln->consensus_string(50), "atgctgat?gacgtacgc????cgctagcact?aga"; 40 41my @dnaseqs = $dna_aln->each_seq; 42is $dnaseqs[0]->display_id, 'n1dna'; 43$dna_aln->verbose(-1); 44my $replicates; 45ok $replicates = &bootstrap_replicates($dna_aln,3); 46 47is scalar @$replicates, 3; 48my $repl_aln = pop @$replicates; 49is $repl_aln->num_sequences, 3; 50 51##use IO::String; 52##use Bio::AlignIO; 53##my $string; 54##my $out = IO::String->new($string); 55## 56##my $strout = Bio::AlignIO->new(-fh => $out,'-format' => 'pfam'); 57##$strout->write_aln($repl_aln); 58##is $string, ""; 59