t/Align/Utilities.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   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
  18 my $DEBUG = test_debug();
  19
  20 my $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
  25 my %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');
  29 my $dna_aln;
  30
  31 ok( $dna_aln = &aa_to_dna_aln($aa_align, \%dnaseqs));
  32 if( $DEBUG ) {
  33         Bio::AlignIO->new(-format=>'clustalw')->write_aln($dna_aln);
  34 }
  35
  36 is $dna_aln->length, 36;
  37 is $dna_aln->num_residues, 99;
  38 is $dna_aln->num_sequences, 3;
  39 is $dna_aln->consensus_string(50), "atgctgat?gacgtacgc????cgctagcact?aga";
  40
  41 my @dnaseqs = $dna_aln->each_seq;
  42 is $dnaseqs[0]->display_id, 'n1dna';
  43 $dna_aln->verbose(-1);
  44 my $replicates;
  45 ok $replicates = &bootstrap_replicates($dna_aln,3);
  46
  47 is scalar @$replicates, 3;
  48 my $repl_aln = pop @$replicates;
  49 is $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, "";