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