t/Perl.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 => 31,
  11                            -requires_module => 'IO::String');
  12
  13         use_ok('Bio::Perl');
  14 }
  15
  16 # Bio::Perl isn't OO so we don't see Bio::Perl->new() here
  17
  18 my ($seq_object,$filename,$blast_report,@seq_object_array);
  19
  20 # will guess file format from extension
  21 $filename = test_input_file('cysprot1.fa');
  22 ok ($seq_object = read_sequence($filename));
  23 isa_ok $seq_object, 'Bio::SeqI';
  24
  25 # forces genbank format
  26 $filename = test_input_file('AF165282.gb');
  27 ok  ($seq_object = read_sequence($filename,'genbank'));
  28 isa_ok $seq_object, 'Bio::SeqI';
  29
  30 # reads an array of sequences
  31 $filename = test_input_file('amino.fa');
  32 is (@seq_object_array = read_all_sequences($filename,'fasta'), 2);
  33 isa_ok $seq_object_array[0], 'Bio::SeqI';
  34 isa_ok $seq_object_array[1], 'Bio::SeqI';
  35
  36 $filename = test_output_file();
  37 ok write_sequence(">$filename",'genbank',$seq_object);
  38 ok ($seq_object = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA","myname","AL12232"));
  39 isa_ok $seq_object, 'Bio::SeqI';
  40
  41 my $trans;
  42
  43 ok ($trans = translate($seq_object));
  44
  45 isa_ok $trans, 'Bio::SeqI';
  46
  47 ok ($trans = translate("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA"));
  48
  49 isa_ok $trans, 'Bio::PrimarySeqI';
  50
  51 ok ($trans = translate_as_string($seq_object));
  52
  53 is $trans, 'IGLGTQFVCYM';
  54
  55 $trans = '';
  56
  57 ok ($trans = translate_as_string("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA"));
  58
  59 is $trans, 'IGLGTQFVCYM';
  60
  61 # we need to keep tests that depend on net connection at the end
  62 # these now run only with BIOPERLDEBUG set
  63
  64 SKIP: {
  65         test_skip(-tests => 12, -requires_networking => 1);
  66
  67         # swissprot
  68         SKIP: {
  69                 eval {
  70                         $seq_object = get_sequence('swissprot',"ROA1_HUMAN");
  71                 };
  72                 if ($@) {
  73                         skip("problem connecting to SwissProt:$@",2);
  74                 } else {
  75                         ok $seq_object;
  76                         isa_ok $seq_object, 'Bio::SeqI';
  77                 }
  78         }
  79
  80     # embl
  81         SKIP: {
  82                 eval {
  83                         $seq_object = get_sequence('embl',"BUM");
  84                 };
  85                 if ($@) {
  86                         skip("problem connecting to EMBL:$@",2);
  87                 } else {
  88                         ok $seq_object;
  89                         isa_ok $seq_object, 'Bio::SeqI';
  90                 }
  91         }
  92
  93         # genbank
  94         SKIP: {
  95                 eval {
  96                         $seq_object = get_sequence('genbank',"AI129902");
  97                 };
  98                 if ($@) {
  99                         skip("problem connecting to GenBank:$@",2);
 100                 } else {
 101                         ok $seq_object;
 102                         isa_ok $seq_object, 'Bio::SeqI';
 103                 }
 104         }
 105
 106     # refseq
 107         SKIP: {
 108                 eval {
 109                         $seq_object = get_sequence('genbank',"NM_006732");
 110                 };
 111                 if( $@ ) {
 112                         skip("problem connecting to RefSeq:$@",2);
 113                 } else {
 114                         ok $seq_object;
 115                         isa_ok $seq_object, 'Bio::SeqI';
 116                 }
 117         }
 118
 119         # genpept
 120         SKIP: {
 121                 eval {
 122                         $seq_object = get_sequence('genpept',"AAC06201");
 123                 };
 124                 if ($@) {
 125                         skip("problem connecting to RefSeq:$@",2);
 126                 } else {
 127                         ok $seq_object;
 128                         isa_ok $seq_object, 'Bio::SeqI';
 129                 }
 130         }
 131
 132     # blast
 133     SKIP: {
 134                 eval {
 135                         $blast_report = blast_sequence($seq_object, 0);
 136                 };
 137                 if ($@) {
 138                         skip("problem connecting to NCBI BLAST:$@",2);
 139                 } else {
 140                         ok $blast_report;
 141                         isa_ok $blast_report, 'Bio::Search::Result::ResultI';
 142                 }
 143     }
 144 }