t/SeqIO/tinyseq.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 => 16,
  11                            -requires_modules => [qw(XML::Parser::PerlSAX XML::Writer)]);
  12
  13         use_ok('Bio::SeqIO::tinyseq');
  14 }
  15
  16 my $file = test_input_file('test.tseq');
  17 my $outfile = test_output_file();
  18
  19 my $instream = Bio::SeqIO->new( -file           => $file,
  20                                 -format         => 'tinyseq' );
  21
  22 my $outstream = Bio::SeqIO->new( -file          => ">$outfile",
  23                                  -format        => 'tinyseq' );
  24
  25 my $seq = $instream->next_seq;
  26 ok(defined $seq);
  27 ok(defined $seq->seq);
  28 is($seq->length, 5830);
  29 is($seq->accession_number,'NM_002253');
  30 ok($seq->species);
  31 is($seq->species->binomial, 'Homo sapiens');
  32 is($seq->species->ncbi_taxid, 9606);
  33 $outstream->write_seq($seq);
  34 undef $outstream;
  35
  36 ok(-s $outfile);
  37
  38 my $reread = Bio::SeqIO->new( -file             => $outfile,
  39                               -format           => 'tinyseq' );
  40
  41 my $seq2 = $reread->next_seq;
  42
  43 ok($seq2);
  44 ok($seq2->seq);
  45 is($seq2->length, 5830);
  46 is($seq2->accession_number, 'NM_002253');
  47 ok($seq2->species);
  48 is($seq2->species->binomial, 'Homo sapiens');
  49 is($seq2->species->ncbi_taxid, 9606);