t/SearchIO/Writer/HSPTableWriter.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 => 8);
  11
  12     use_ok('Bio::SearchIO');
  13     use_ok('Bio::SearchIO::Writer::HSPTableWriter');
  14 }
  15
  16 my ($searchio, $result, $hit, $hsp);
  17
  18 $searchio = Bio::SearchIO->new('-format' => 'blast',
  19     '-file'   => test_input_file('HUMBETGLOA.tblastx'));
  20
  21 $result = $searchio->next_result;
  22
  23 isa_ok($result,'Bio::Search::Result::ResultI');
  24 $hit = $result->next_hit;
  25 is($hit->accession, 'AE000479');
  26 is($hit->bits, 33.6);
  27 $hsp = $hit->next_hsp;
  28 is($hit->hsp->bits,$hsp->bits);
  29 isa_ok($hsp->get_aln,'Bio::Align::AlignI');
  30
  31 my $writer = Bio::SearchIO::Writer::HSPTableWriter->new(
  32 -columns => [qw(
  33     query_name
  34     query_length
  35     hit_name
  36     hit_length
  37     rank
  38     frac_identical_query
  39     expect
  40     )]  );
  41
  42 my $outfile = test_output_file();
  43 my $out = Bio::SearchIO->new(-writer => $writer,
  44              -file   => ">$outfile");
  45 $out->write_result($result, 1);
  46 ok(-s $outfile);
  47
  48 # tests checking file output?