t/SeqIO/tinyseq.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use Bio::Root::Test;
   8
   9     test_begin(-tests => 16,
  10                -requires_modules => [qw(XML::Parser::PerlSAX XML::Writer)]);
  11
  12     use_ok('Bio::SeqIO::tinyseq');
  13 }
  14
  15 my $file    = test_input_file('test.tseq');
  16 my $outfile = test_output_file();
  17
  18 my $instream = Bio::SeqIO->new( -file    => $file,
  19                                 -format  => 'tinyseq' );
  20
  21 my $outstream = Bio::SeqIO->new( -file   => ">$outfile",
  22                                  -format => 'tinyseq' );
  23
  24 my $seq = $instream->next_seq;
  25 ok(defined $seq);
  26 ok(defined $seq->seq);
  27 is($seq->length, 5830);
  28 is($seq->accession_number,'NM_002253');
  29 ok($seq->species);
  30 is($seq->species->binomial, 'Homo sapiens');
  31 is($seq->species->ncbi_taxid, 9606);
  32 $outstream->write_seq($seq);
  33 undef $outstream;
  34
  35 ok(-s $outfile);
  36
  37 my $reread = Bio::SeqIO->new( -file   => $outfile,
  38                               -format => 'tinyseq' );
  39
  40 my $seq2 = $reread->next_seq;
  41
  42 ok($seq2);
  43 ok($seq2->seq);
  44 is($seq2->length, 5830);
  45 is($seq2->accession_number, 'NM_002253');
  46 ok($seq2->species);
  47 is($seq2->species->binomial, 'Homo sapiens');
  48 is($seq2->species->ncbi_taxid, 9606);