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 => 24,
  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('factor7.embl');
  47
  48 $result = $db->build_index(glob($dir));
  49 ok($result);
  50 $seq = $db->get_Seq_by_id('HSCFVII');
  51 ok($seq);
  52 is($seq->length,12850);
  53
  54 # deal with wantarray conditions
  55 $seq = $db->get_Seq_by_acc('J02933');
  56 ok($seq && ref($seq));
  57 is($seq->length,12850);
  58
  59
  60 undef $db;
  61
  62 $db = Bio::DB::Flat->new(-directory  => $tmpdir,
  63                          -index      => 'binarysearch',
  64                          -format     => 'fasta',
  65                          -dbname     => 'mybinfa',
  66                          -verbose    => $verbose,
  67                          -write_flag => 1
  68                          );
  69
  70 $dir= test_input_file('dbfa', '1.fa');
  71 $result = $db->build_index($dir);
  72 ok($result);
  73 $seq = $db->get_Seq_by_id('AW057119');
  74 ok($seq);
  75 is($seq->length,808);
  76 undef $db;
  77
  78 $db = Bio::DB::Flat->new(-directory  => $tmpdir,
  79                          -index      => 'binarysearch',
  80                          -format     => 'swiss',
  81                          -dbname     => 'mybinswiss',
  82                          -verbose    => $verbose,
  83                          -write_flag => 1
  84                          );
  85 $dir= test_input_file('swiss.dat');
  86 $result = $db->build_index($dir);
  87
  88 ok($result);
  89 $seq = $db->get_Seq_by_id('ACON_CAEEL');
  90 ok($seq);
  91 is($seq->length,788);
  92
  93 $seq = $db->get_Seq_by_id('ACON_CAEEL');
  94 ok($seq && ref($seq));
  95
  96 undef $db;
  97
  98 $db = Bio::DB::Flat->new(-directory  => $tmpdir,
  99                          -index      => 'binarysearch',
 100                          -format     => 'fasta',
 101                                                                  -dbname     => 'myfasta',
 102                          -verbose    => $verbose,
 103                          -write_flag => 1 );
 104
 105 $dir = test_input_file('tmp.fst');
 106 $result = $db->build_index(glob($dir));
 107 ok($result);
 108 $seq = $db->get_Seq_by_id('TEST00004');
 109 is($seq->length,98);
 110
 111 undef $db;
 112
 113 $db = Bio::DB::Flat->new(-directory  => $tmpdir,
 114                          -index      => 'bdb',
 115                          -format     => 'fasta',
 116                                                                  -dbname     => 'mybfasta',
 117                          -verbose    => $verbose,
 118                          -write_flag => 1 );
 119
 120 $dir = test_input_file('tmp.fst');
 121 $result = $db->build_index(glob($dir));
 122 ok($result);
 123 for my $id ( qw(TEST00001 TEST00002 TEST00003 TEST00004) ) {
 124         $seq = $db->get_Seq_by_id($id);
 125         is($seq->length,98);
 126 }