branch-1-6/t/Assembly/Assembly.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use lib '.';
   8     use Bio::Root::Test;
   9
  10     test_begin(-tests => 51,
  11         -requires_module => 'DB_File');
  12
  13         use_ok('Bio::Assembly::IO');
  14 }
  15
  16 #
  17 # Testing IO
  18 #
  19
  20 #
  21 # Some PHRAP input
  22 #
  23
  24 my $in = Bio::Assembly::IO->new
  25         (-file => test_input_file('consed_project','edit_dir','test_project.phrap.out'));
  26
  27 isa_ok($in, 'Bio::Assembly::IO');
  28
  29 my $sc;
  30
  31 TODO: {
  32         local $TODO = "phrap parser doesn't include the sequence string in the sequence objects.";
  33         $in->verbose(2);
  34         eval {$sc = $in->next_assembly};
  35         ok(!$@);
  36 }
  37
  38 $in = Bio::Assembly::IO->new
  39         (-file => test_input_file('consed_project','edit_dir','test_project.phrap.out'));
  40
  41 $in->verbose(-1);
  42
  43 $sc = $in->next_assembly;
  44
  45 isa_ok($sc,
  46            'Bio::Assembly::Scaffold');
  47
  48 #
  49 # Testing Scaffold
  50 #
  51
  52 is $sc->id, "NoName";
  53 is $sc->id('test'), "test";
  54
  55 isa_ok($sc->annotation, 'Bio::AnnotationCollectionI');
  56 is $sc->annotation->get_all_annotation_keys, 0,"no annotations in Annotation collection?";
  57 is $sc->get_nof_contigs, 1;
  58 is $sc->get_nof_sequences_in_contigs, 2;
  59 is($sc->get_nof_singlets, 2, "get_nof_singlets");
  60 is($sc->get_contig_seq_ids, 2, "get_contig_seq_ids");
  61 is($sc->get_contig_ids, 1, "get_contig_ids");
  62 is($sc->get_singlet_ids, 2, "get_singlet_ids");
  63
  64 #
  65 # Testing Contig
  66 #
  67
  68 #
  69 # Testing ContigAnalysis
  70 #
  71
  72 #
  73 # Testing Ace
  74 #
  75
  76 my $aio = Bio::Assembly::IO->new(
  77         -file=>test_input_file('consed_project','edit_dir','test_project.fasta.screen.ace.2'),
  78         -format=>'ace',
  79 );
  80
  81 my $assembly = $aio->next_assembly();
  82
  83 my @contigs = $assembly->all_contigs();
  84
  85 my $direction = $contigs[0]->strand;
  86 is $direction, 1;
  87
  88 my $features =  $contigs[0]->get_features_collection;
  89 my @contig_features = $features->get_all_features;
  90 is @contig_features, 8;
  91
  92 my @annotations = grep {$_->primary_tag eq 'Annotation'} @contig_features;
  93 is @annotations, 2;
  94 my $had_tag = 0;
  95 foreach my $an (@annotations) {
  96         if ($an->has_tag('extra_info')) {
  97                 $had_tag++;
  98                 is (($an->get_tag_values('extra_info'))[0], "contig extra\ninfo\n");
  99         }
 100         elsif ($an->has_tag('comment')){
 101                 $had_tag++;
 102                 is (($an->get_tag_values('comment'))[0], "contig tag\ncomment\n");
 103         }
 104 }
 105 is $had_tag, 2;
 106
 107 is $assembly->get_nof_contigs, 1;
 108 is $assembly->get_nof_sequences_in_contigs, 2;
 109 is($assembly->get_nof_singlets, 0, "get_nof_singlets");
 110 is($assembly->get_contig_seq_ids, 2, "get_contig_seq_ids");
 111 is($assembly->get_contig_ids, 1, "get_contig_ids");
 112 is($assembly->get_singlet_ids, 0, "get_singlet_ids");
 113
 114
 115 $aio = Bio::Assembly::IO->new(
 116         -file=>test_input_file('assembly_with_singlets.ace'),
 117         -format=>'ace',
 118 );
 119 $assembly = $aio->next_assembly();
 120 is $assembly->get_nof_contigs, 3;
 121 my @ace_contigs = $assembly->all_contigs();
 122 isa_ok $ace_contigs[0], "Bio::Assembly::Contig",'the contig is a Bio::Assembly::Contig';
 123 is $assembly->get_nof_sequences_in_contigs, 6;
 124 is($assembly->get_nof_singlets, 33, "get_nof_singlets");
 125 my @ace_singlets = $assembly->all_singlets();
 126 isa_ok $ace_singlets[0], "Bio::Assembly::Contig",'the singlet is a Bio::Assembly::Contig';
 127 isa_ok $ace_singlets[0], "Bio::Assembly::Singlet",'the singlet is a Bio::Assembly::Singlet';
 128 is($assembly->get_contig_seq_ids, 6, "get_contig_seq_ids");
 129 is($assembly->get_contig_ids, 3, "get_contig_ids");
 130 is($assembly->get_singlet_ids, 33, "get_singlet_ids");
 131
 132
 133
 134
 135 #
 136 # Testing TIGR format
 137 #
 138
 139 # Importing an assembly
 140
 141 my $asm_in = Bio::Assembly::IO->new(
 142     -file => test_input_file("sample_dataset.tasm "),
 143     -format=>'tigr'
 144 );
 145 my $scaf_in = $asm_in->next_assembly;
 146
 147 isa_ok($scaf_in, 'Bio::Assembly::Scaffold');
 148 is($scaf_in->id, 'NoName');
 149 is($scaf_in->get_nof_contigs, 13);
 150 is($scaf_in->get_nof_sequences_in_contigs, 36);
 151 is($scaf_in->get_nof_singlets, 0);
 152 my @seqids = sort qw(sdsu|SDSU1_RFPERU_001_A09.x01.phd.1
 153 sdsu|SDSU1_RFPERU_001_B03.x01.phd.1 sdsu|SDSU1_RFPERU_001_B04.x01.phd.1
 154 sdsu|SDSU1_RFPERU_001_E04.x01.phd.1 sdsu|SDSU_RFPERU_002_A01.x01.phd.1
 155 sdsu|SDSU_RFPERU_002_B07.x01.phd.1 sdsu|SDSU_RFPERU_002_C12.x01.phd.1
 156 sdsu|SDSU_RFPERU_002_D08.x01.phd.1 sdsu|SDSU_RFPERU_002_H12.x01.phd.1
 157 sdsu|SDSU_RFPERU_003_G09.x01.phd.1 sdsu|SDSU_RFPERU_004_H12.x01.phd.1
 158 sdsu|SDSU_RFPERU_005_F02.x01.phd.1 sdsu|SDSU_RFPERU_006_D03.x01.phd.1
 159 sdsu|SDSU_RFPERU_006_E04.x01.phd.1 sdsu|SDSU_RFPERU_006_E05.x01.phd.1
 160 sdsu|SDSU_RFPERU_006_H08.x01.phd.1 sdsu|SDSU_RFPERU_007_E09.x01.phd.1
 161 sdsu|SDSU_RFPERU_007_F06.x01.phd.1 sdsu|SDSU_RFPERU_008_B02.x01.phd.1
 162 sdsu|SDSU_RFPERU_009_E07.x01.phd.1 sdsu|SDSU_RFPERU_010_B05.x01.phd.1
 163 sdsu|SDSU_RFPERU_010_B06.x01.phd.1 sdsu|SDSU_RFPERU_010_C09.x01.phd.1
 164 sdsu|SDSU_RFPERU_010_D10.x01.phd.1 sdsu|SDSU_RFPERU_012_H02.x01.phd.1
 165 sdsu|SDSU_RFPERU_013_B05.x01.phd.1 sdsu|SDSU_RFPERU_013_C07.x01.phd.1
 166 sdsu|SDSU_RFPERU_013_C08.x01.phd.1 sdsu|SDSU_RFPERU_013_G10.x01.phd.1
 167 sdsu|SDSU_RFPERU_013_H05.x01.phd.1 sdsu|SDSU_RFPERU_014_H06.x01.phd.1
 168 sdsu|SDSU_RFPERU_015_A05.x01.phd.1 sdsu|SDSU_RFPERU_015_C06.x01.phd.1
 169 sdsu|SDSU_RFPERU_015_E04.x01.phd.1 sdsu|SDSU_RFPERU_015_G04.x01.phd.1
 170 sdsu|SDSU_RFPERU_015_H03.x01.phd.1);
 171 my @contigids = sort qw(106 144 148 17 185 2 210 36 453 500 613 668 93);
 172 is_deeply([sort $scaf_in->get_contig_seq_ids], \@seqids);
 173 is_deeply([sort $scaf_in->get_contig_ids], \@contigids);
 174 is_deeply([$scaf_in->get_singlet_ids], []);
 175 isa_ok($scaf_in->get_seq_by_id('sdsu|SDSU1_RFPERU_001_A09.x01.phd.1'),'Bio::LocatableSeq');
 176 my $contig = $scaf_in->get_contig_by_id('106');
 177 isa_ok($contig,'Bio::Assembly::Contig');
 178 # check Contig object SeqFeature::Collection
 179 # should add more specific Contig tests...
 180 my @sfs = $contig->get_features_collection->get_all_features;
 181 is(scalar(@sfs), 5);
 182 my %primary_tags = map { $_->primary_tag => 1 } @sfs;
 183 ok exists $primary_tags{'_aligned_coord:sdsu|SDSU_RFPERU_006_E04.x01.phd.1'};
 184 is($sfs[1]->seq_id(), undef); # should this be undef?
 185
 186 isa_ok($scaf_in->annotation, 'Bio::AnnotationCollectionI');
 187 is($scaf_in->annotation->get_all_annotation_keys, 0,"no annotations in Annotation collection?");
 188
 189 # Exporting an assembly
 190
 191 my $asm_outfile = test_output_file();
 192 my $asm_out = Bio::Assembly::IO->new(
 193     -file=> ">$asm_outfile",
 194     -format=>'tigr'
 195 );
 196
 197 ok $asm_out->write_assembly( -scaffold => $scaf_in);
 198