t/Hmmer.t

   1 #!/usr/local/bin/perl
   2 #-*-Perl-*-
   3 # ## Bioperl Test Harness Script for Modules
   4 # #
   5 use strict;
   6 BEGIN {
   7    eval { require Test; };
   8    if( $@ ) {
   9       use lib 't';
  10    }
  11    use Test;
  12    use vars qw($NTESTS);
  13    $NTESTS = 20;
  14    plan tests => $NTESTS;
  15 }
  16
  17 use Bio::Tools::Run::Hmmer;
  18 use Bio::Root::IO;
  19 use Bio::SeqIO;
  20 use Bio::AlignIO;
  21 use Bio::Seq;
  22
  23 END {
  24    foreach ( $Test::ntest..$NTESTS ) {
  25        skip('Unable to run Hmmer tests, exe may not be installed',1);
  26    }
  27    unlink Bio::Root::IO->catfile(qw(t data hmmer.hmm));
  28 }
  29 ok(1);
  30
  31 my $verbose = 1 if $ENV{'BIOPERLDEBUG'};
  32
  33 my $db =  Bio::Root::IO->catfile("t","data","pfam_sample_R11");
  34 my @params = ('DB'=>$db,'E'=>5,'program'=>'hmmpfam','A'=>2,'-verbose' => $verbose);
  35
  36 #test HMMPFAM
  37 my  $factory = Bio::Tools::Run::Hmmer->new(@params);
  38 ok $factory->isa('Bio::Tools::Run::Hmmer');
  39 ok $factory->E, 5;
  40 my $prot_file=  Bio::Root::IO->catfile("t","data","hmmpfam_protein_input");
  41
  42 my $seq1 = Bio::Seq->new();
  43 my $seqstream = Bio::SeqIO->new(-file   => $prot_file,
  44                                 -format => 'fasta');
  45 $seq1 = $seqstream->next_seq();
  46
  47 my $hmmpfam_present = $factory->executable();
  48
  49 unless ($hmmpfam_present) {
  50        warn("hmmpfam  program not found. Skipping tests $Test::ntest to $NTESTS.\n");
  51        exit 0;
  52 }
  53
  54 my $searchio = $factory->run($seq1);
  55
  56 my @feat;
  57 while (my $result = $searchio->next_result){
  58   while(my $hit = $result->next_hit){
  59     while (my $hsp = $hit->next_hsp){
  60       push @feat, $hsp;
  61     }
  62   }
  63 }
  64
  65 ok $feat[0]->isa('Bio::SeqFeatureI');
  66 ok ($feat[0]->feature1->start,25);
  67 ok ($feat[0]->feature1->end,92);
  68 ok ($feat[0]->feature2->start,1);
  69 ok ($feat[0]->feature2->end,124);
  70
  71 #test HMMSEARCH
  72 @params = ('HMM'=>$db,'E'=>5,'program'=>'hmmsearch','-verbose' => $verbose);
  73 $factory = Bio::Tools::Run::Hmmer->new(@params);
  74 ok $factory->isa('Bio::Tools::Run::Hmmer');
  75 ok $factory->E, 5;
  76 $prot_file=  Bio::Root::IO->catfile("t","data","hmmpfam_protein_input");
  77
  78 $seq1 = Bio::Seq->new();
  79 $seqstream = Bio::SeqIO->new(-file   => $prot_file,
  80                              -format => 'fasta');
  81 $seq1 = $seqstream->next_seq();
  82
  83 my $hmmsearch = $factory->executable();
  84
  85 unless ($hmmsearch) {
  86        warn("hmmsearch program not found. Skipping tests $Test::ntest to $NTESTS.\n");
  87        exit 0;
  88 }
  89 $searchio = $factory->run($seq1);
  90 @feat= ();
  91 while (my $result = $searchio->next_result){
  92   while(my $hit = $result->next_hit){
  93     while (my $hsp = $hit->next_hsp){
  94       push @feat, $hsp;
  95     }
  96   }
  97 }
  98
  99 ok $feat[0]->isa('Bio::SeqFeatureI');
 100 ok ($feat[0]->feature1->start,1);
 101 ok ($feat[0]->feature1->end,124);
 102 ok ($feat[0]->feature2->start,25);
 103 ok ($feat[0]->feature2->end,92);
 104
 105 #test HMMBUILD
 106 my $hmmout=  Bio::Root::IO->catfile("t","data","hmmer.hmm");
 107 @params = ('HMM'=>$hmmout,'program'=>'hmmbuild');
 108 $factory = Bio::Tools::Run::Hmmer->new(@params);
 109 ok $factory->isa('Bio::Tools::Run::Hmmer');
 110 my $aln_file=  Bio::Root::IO->catfile("t","data","cysprot.msf");
 111 my $aio = Bio::AlignIO->new(-file=>$aln_file,-format=>'msf');
 112 my $aln = $aio->next_aln;
 113 $factory->run($aln);
 114 ok -e $hmmout;
 115
 116
 117
 118 #test HMMALIGN
 119 $hmmout=  Bio::Root::IO->catfile("t","data","hmmer.hmm");
 120 @params = ('HMM'=>$hmmout,'program'=>'hmmalign');
 121 $factory = Bio::Tools::Run::Hmmer->new(@params);
 122 ok $factory->isa('Bio::Tools::Run::Hmmer');
 123 my $seqfile=  Bio::Root::IO->catfile("t","data","cysprot1a.fa");
 124 my $seqio = Bio::SeqIO->new(-file  => $seqfile,
 125                             -format=> 'fasta');
 126 my @seqs;
 127 while( my $seq = $seqio->next_seq ) {
 128     push @seqs, $seq;
 129 }
 130 $aio = $factory->run(@seqs);
 131 $aln = $aio->next_aln;
 132 ok($aln);
 133 #$aio = Bio::AlignIO->new(-format => 'clustalw');
 134 #$aio->write_aln($aln);
 135 ok($aln->each_seq, 3);
 136
 137 1;
 138