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, -requires_module => 'LWP::UserAgent');
  66
  67         # swissprot
  68         SKIP: {
  69                 test_skip(-tests => 2, -requires_module => 'Data::Stag');
  70                 eval {
  71                         $seq_object = get_sequence('swissprot',"ROA1_HUMAN");
  72                 };
  73                 if ($@) {
  74                         skip("problem connecting to SwissProt:$@",2);
  75                 } else {
  76                         ok $seq_object;
  77                         isa_ok $seq_object, 'Bio::SeqI';
  78                 }
  79         }
  80
  81     # embl
  82         SKIP: {
  83                 eval {
  84                         $seq_object = get_sequence('embl',"HSFOS");
  85                 };
  86                 if ($@) {
  87                         skip("problem connecting to EMBL:$@",2);
  88                 } else {
  89                         ok $seq_object;
  90                         isa_ok $seq_object, 'Bio::SeqI';
  91                 }
  92         }
  93
  94         # genbank
  95         SKIP: {
  96                 eval {
  97                         $seq_object = get_sequence('genbank',"AI129902");
  98                 };
  99                 if ($@) {
 100                         skip("problem connecting to GenBank:$@",2);
 101                 } else {
 102                         ok $seq_object;
 103                         isa_ok $seq_object, 'Bio::SeqI';
 104                 }
 105         }
 106
 107     # refseq
 108         SKIP: {
 109                 eval {
 110                         $seq_object = get_sequence('genbank',"NM_006732");
 111                 };
 112                 if( $@ ) {
 113                         skip("problem connecting to RefSeq:$@",2);
 114                 } else {
 115                         ok $seq_object;
 116                         isa_ok $seq_object, 'Bio::SeqI';
 117                 }
 118         }
 119
 120         # genpept
 121         SKIP: {
 122                 eval {
 123                         $seq_object = get_sequence('genpept',"AAC06201");
 124                 };
 125                 if ($@) {
 126                         skip("problem connecting to RefSeq:$@",2);
 127                 } else {
 128                         ok $seq_object;
 129                         isa_ok $seq_object, 'Bio::SeqI';
 130                 }
 131         }
 132
 133     # blast
 134     SKIP: {
 135                 eval {
 136                         $blast_report = blast_sequence($seq_object, 0);
 137                 };
 138                 if ($@) {
 139                         skip("problem connecting to NCBI BLAST:$@",2);
 140                 } else {
 141                         ok $blast_report;
 142                         isa_ok $blast_report, 'Bio::Search::Result::ResultI';
 143                 }
 144     }
 145 }