t/TCoffee.t

   1 # -*-Perl-*-
   2 ## Bioperl Test Harness Script for Modules
   3 ## $Id$
   4
   5 use strict;
   6 use vars qw($NUMTESTS);
   7 BEGIN {
   8     eval { require Test; };
   9     if( $@ ) {
  10         use lib 't';
  11     }
  12     use Test;
  13
  14     $NUMTESTS = 22;
  15     plan tests => $NUMTESTS;
  16 }
  17
  18 END { unlink qw(cysprot.dnd cysprot1a.dnd) }
  19
  20 use Bio::Tools::Run::Alignment::TCoffee;
  21 use Bio::SimpleAlign;
  22 use Bio::AlignIO;
  23 use Bio::SeqIO;
  24 use Bio::Root::IO;
  25
  26 END {
  27     for ( $Test::ntest..$NUMTESTS ) {
  28         skip("TCoffee program not found. Skipping.\n",1);
  29     }
  30     unlink("t_coffee.log");
  31 }
  32
  33 ok(1);
  34
  35 my @params;
  36 my  $factory = Bio::Tools::Run::Alignment::TCoffee->new(@params);
  37
  38 ok ($factory =~ /Bio::Tools::Run::Alignment::TCoffee/);
  39
  40 my $ktuple = 3;
  41 $factory->ktuple($ktuple);
  42
  43 my $new_ktuple = $factory->ktuple();
  44 ok $new_ktuple, 3, " couldn't set factory parameter";
  45
  46 my $what_matrix = $factory->matrix();
  47 ok $what_matrix, qr/BLOSUM/i, "couldn't get factory parameter";
  48
  49 my $bequiet = 1;
  50 $factory->quiet($bequiet);  # Suppress tcoffee messages to terminal
  51
  52 my $inputfilename = Bio::Root::IO->catfile("t","data","cysprot.fa");
  53 my $aln;
  54
  55
  56 my $coffee_present = $factory->executable();
  57 unless ($coffee_present) {
  58     warn "tcoffee program not found. Skipping tests $Test::ntest to $NUMTESTS.\n";
  59     exit(0);
  60 }
  61 my $version = $factory->version;
  62 ok ($version >= 1.22, 1, "Code tested only on t_coffee versions > 1.22" );
  63 $aln = $factory->align($inputfilename);
  64 ok($aln);
  65 ok( $aln->no_sequences, 7);
  66
  67 my $str = Bio::SeqIO->new('-file' =>
  68                           Bio::Root::IO->catfile("t","data","cysprot.fa"),
  69                           '-format' => 'Fasta');
  70 my @seq_array =();
  71
  72 while ( my $seq = $str->next_seq() ) {
  73     push (@seq_array, $seq) ;
  74 }
  75
  76 my $seq_array_ref = \@seq_array;
  77
  78 $aln = $factory->align($seq_array_ref);
  79 ok $aln->no_sequences, 7;
  80 my $s1_perid = $aln->average_percentage_identity;
  81
  82
  83 my $profile1 = Bio::Root::IO->catfile("t","data","cysprot1a.msf");
  84 my $profile2 = Bio::Root::IO->catfile("t","data","cysprot1b.msf");
  85 $aln = $factory->profile_align($profile1,$profile2);
  86 ok $aln->no_sequences, 7;
  87
  88 my $str1 = Bio::AlignIO->new(-file=> Bio::Root::IO->catfile("t","data","cysprot1a.msf"));
  89 my $aln1 = $str1->next_aln();
  90 ok $aln1->no_sequences, 3;
  91
  92 my $str2 = Bio::AlignIO->new(-file=> Bio::Root::IO->catfile("t","data","cysprot1b.msf"));
  93 my $aln2 = $str2->next_aln();
  94 ok $aln2->no_sequences, 4;
  95
  96 $aln = $factory->profile_align($aln1,$aln2);
  97 ok $aln->no_sequences, 7;
  98
  99
 100 $str1 = Bio::AlignIO->new(-file=> Bio::Root::IO->catfile("t","data","cysprot1a.msf"));
 101 $aln1 = $str1->next_aln();
 102 $str2 = Bio::SeqIO->new(-file=> Bio::Root::IO->catfile("t","data","cysprot1b.fa"));
 103 my $seq = $str2->next_seq();
 104
 105 ok $aln1->no_sequences, 3;
 106 ok( int($aln1->average_percentage_identity), 39);
 107 $aln = $factory->profile_align($aln1,$seq);
 108 ok( $aln->no_sequences, 4);
 109 if( $version <= 1.22 ) {
 110     ok( $aln->overall_percentage_identity > 18);
 111     ok( int($aln->average_percentage_identity), 44);
 112 } else {
 113     my $overall = int($aln->overall_percentage_identity);
 114     ok( $overall >=21 && $overall <= 23, 1, 'expect 21 >= val >= 23');
 115     my $avg = int($aln->average_percentage_identity);
 116     ok( $avg == 47 || $avg ==48, 1, 'expect 47 or 48');
 117 }
 118
 119 # test new 'run' generic running of factory
 120
 121 $aln = $factory->run('-type' => 'profile',
 122                      '-profile' => $aln1,
 123                      '-seq'  => Bio::Root::IO->catfile("t","data","cysprot1b.fa"));
 124
 125 ok( $aln->no_sequences, 7);
 126 if( $version <= 1.22 ) {
 127     ok( $aln->overall_percentage_identity > 18);
 128     ok( int($aln->average_percentage_identity), 44);
 129 } else {
 130     my $overall = int $aln->overall_percentage_identity;
 131     ok($overall == 14 || $overall == 13,1,'expect 13 or 14');
 132     my $avg = int($aln->average_percentage_identity);
 133     ok($avg == 41 || $avg == 42, 1, 'expect 41 or 42');
 134 }
 135
 136 $aln = $factory->run('-type' => 'align',
 137                      '-seq'  => Bio::Root::IO->catfile("t","data","cysprot.fa"));
 138 ok ($aln->no_sequences, 7);
 139 ok ($aln->percentage_identity,$s1_perid); #calculated before