t/flat.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5 use File::Temp qw(tempdir);
   6
   7 BEGIN {
   8     use lib 't/lib';
   9         use BioperlTest;
  10
  11         test_begin(-tests => 18,
  12                                   -requires_module => 'DB_File');
  13
  14         use_ok('Bio::DB::Flat');
  15 }
  16
  17 my $verbose = test_debug();
  18
  19 #First of all we need to create an flat db
  20
  21 my $tmpdir = tempdir( CLEANUP => 1 );
  22
  23 my $db = Bio::DB::Flat->new(-directory  => $tmpdir,
  24                             -index      => 'bdb',
  25                             -dbname     => 'mydb',
  26                             -format     => 'fasta',
  27                             -verbose    => $verbose,
  28                             -write_flag => 1
  29                             );
  30 ok($db);
  31 my $dir = test_input_file('AAC12660.fa');
  32 my $result = $db->build_index(glob($dir));
  33 ok($result);
  34
  35 # Now let's get the sequence out again
  36 my $seq = $db->get_Seq_by_id('AAC12660');
  37 ok($seq);
  38 is($seq->length,504);
  39 undef $db;
  40
  41 $db = Bio::DB::Flat->new(-directory  => $tmpdir,
  42                          -index      => 'bdb',
  43                          -format     => 'embl',
  44                                                                  -dbname     => 'myembl',
  45                          -verbose    => $verbose,
  46                          -write_flag => 1
  47                          );
  48
  49 $dir= test_input_file('factor7.embl');
  50
  51 $result = $db->build_index(glob($dir));
  52 ok($result);
  53 $seq = $db->get_Seq_by_id('HSCFVII');
  54 ok($seq);
  55 is($seq->length,12850);
  56
  57 # deal with wantarray conditions
  58 $seq = $db->get_Seq_by_acc('J02933');
  59 ok($seq && ref($seq));
  60 is($seq->length,12850);
  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 $db = Bio::DB::Flat->new(-directory  => $tmpdir,
  82                          -index      => 'binarysearch',
  83                          -format     => 'swiss',
  84                          -dbname     => 'mybinswiss',
  85                          -verbose    => $verbose,
  86                          -write_flag => 1
  87                          );
  88 $dir= test_input_file('swiss.dat');
  89 $result = $db->build_index($dir);
  90
  91 ok($result);
  92 $seq = $db->get_Seq_by_id('ACON_CAEEL');
  93 ok($seq);
  94 is($seq->length,788);
  95
  96 $seq = $db->get_Seq_by_id('ACON_CAEEL');
  97 ok($seq && ref($seq));
  98
  99 undef $db;
 100
 101 $db = Bio::DB::Flat->new(-directory  => $tmpdir,
 102                          -index      => 'binarysearch',
 103                          -format     => 'fasta',
 104                                                                  -dbname     => 'myfasta',
 105                          -verbose    => $verbose,
 106                          -write_flag => 1
 107                          );
 108
 109 $dir = test_input_file('tmp.fst');
 110 $result = $db->build_index(glob($dir));
 111 ok($result);
 112