t/LocalDB/Flat.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 => 27,
  10                -requires_module => 'DB_File');
  11
  12     use_ok('Bio::DB::Flat');
  13 }
  14
  15 my $verbose = test_debug();
  16
  17 # First of all we need to create an flat db
  18
  19 my $tmpdir = test_output_dir();
  20
  21 my $db = Bio::DB::Flat->new(-directory  => $tmpdir,
  22                             -index      => 'bdb',
  23                             -dbname     => 'mydb',
  24                             -format     => 'fasta',
  25                             -verbose    => $verbose,
  26                             -write_flag => 1 );
  27 ok($db);
  28 my $dir = test_input_file('AAC12660.fa');
  29 my $result = $db->build_index(glob($dir));
  30 ok($result);
  31
  32 # Now let's get the sequence out again
  33 my $seq = $db->get_Seq_by_id('AAC12660');
  34 ok($seq);
  35 is($seq->length,504);
  36 undef $db;
  37
  38 $db = Bio::DB::Flat->new(-directory  => $tmpdir,
  39                          -index      => 'bdb',
  40                          -format     => 'embl',
  41                          -dbname     => 'myembl',
  42                          -verbose    => $verbose,
  43                          -write_flag => 1 );
  44
  45 $dir= test_input_file('cds_sample.embl');
  46
  47 $result = $db->build_index(glob($dir));
  48
  49 is ($db->get_all_primary_ids, 1);
  50 #is ($db->get_all_accs, 1);
  51 ok($result);
  52 $seq = $db->get_Seq_by_id('EAL24309');
  53 ok($seq);
  54 is($seq->length,192);
  55
  56 # deal with wantarray conditions
  57 $seq = $db->get_Seq_by_acc('CH236947.1');
  58 ok($seq && ref($seq));
  59 is($seq->length,192);
  60
  61 undef $db;
  62
  63 $db = Bio::DB::Flat->new(-directory  => $tmpdir,
  64                          -index      => 'binarysearch',
  65                          -format     => 'fasta',
  66                          -dbname     => 'mybinfa',
  67                          -verbose    => $verbose,
  68                          -write_flag => 1
  69                          );
  70
  71 $dir = test_input_file('dbfa', '1.fa');
  72 $result = $db->build_index($dir);
  73 ok($result);
  74 $seq = $db->get_Seq_by_id('AW057119');
  75 ok($seq);
  76 is($seq->length, 808);
  77 $seq = $db->get_Seq_by_id('AW057118');
  78 ok($seq);
  79 is($seq->length, 299);
  80
  81 undef $db;
  82
  83 SKIP: {
  84     test_skip(-tests => 4, -requires_module => 'Data::Stag');
  85     $db = Bio::DB::Flat->new(-directory  => $tmpdir,
  86                              -index      => 'binarysearch',
  87                              -format     => 'swiss',
  88                              -dbname     => 'mybinswiss',
  89                              -verbose    => $verbose,
  90                              -write_flag => 1
  91                              );
  92     $dir= test_input_file('swiss.dat');
  93     $result = $db->build_index($dir);
  94
  95     ok($result);
  96     $seq = $db->get_Seq_by_id('ACON_CAEEL');
  97     ok($seq);
  98     is($seq->length,788);
  99
 100     $seq = $db->get_Seq_by_id('ACON_CAEEL');
 101     ok($seq && ref($seq));
 102
 103     undef $db;
 104 }
 105 $db = Bio::DB::Flat->new(-directory  => $tmpdir,
 106                          -index      => 'binarysearch',
 107                          -format     => 'fasta',
 108                          -dbname     => 'myfasta',
 109                          -verbose    => $verbose,
 110                          -write_flag => 1 );
 111
 112 $dir = test_input_file('tmp.fst');
 113 $result = $db->build_index(glob($dir));
 114 ok($result);
 115 $seq = $db->get_Seq_by_id('TEST00004');
 116 is($seq->length,98);
 117
 118 undef $db;
 119
 120 $db = Bio::DB::Flat->new(-directory  => $tmpdir,
 121                          -index      => 'bdb',
 122                          -format     => 'fasta',
 123                          -dbname     => 'mybfasta',
 124                          -verbose    => $verbose,
 125                          -write_flag => 1 );
 126
 127 $dir = test_input_file('tmp.fst');
 128 $result = $db->build_index(glob($dir));
 129 ok($result);
 130 for my $id ( qw(TEST00001 TEST00002 TEST00003 TEST00004) ) {
 131     $seq = $db->get_Seq_by_id($id);
 132     is($seq->length,98);
 133 }