Bio-MUST-Drivers

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t/blast.t  view on Meta::CPAN

        \&filter, 'wrote expected tabular BLASTP report';
    $tab_parser->remove;

    # 2c. XML format
    my $xml_parser = $db->blast($query, {
        -evalue => 1e-10,
        -outfmt => 5,
    } );
    isa_ok($xml_parser, 'Bio::FastParsers::Blast::Xml');

    cmp_ok $xml_parser->blast_output->count_iterations, '==', 7,
        'got expected number of iterations';

    $report_xml = $xml_parser->filename;
    explain $report_xml;
    compare_filter_ok $report_xml, file('test', 'report.blastp.xml'),
        \&filter, 'wrote expected XML BLASTP report';
    $xml_parser->remove;

    # blastdbcmd from temporary database
    my @ids = qw(seq2 seq4 seq6);
    my $seqs = $db->blastdbcmd( \@ids );

test/old-blast/report.blastp.xml  view on Meta::CPAN

  <BlastOutput_query-len>881</BlastOutput_query-len>
  <BlastOutput_param>
    <Parameters>
      <Parameters_matrix>BLOSUM62</Parameters_matrix>
      <Parameters_expect>1e-10</Parameters_expect>
      <Parameters_gap-open>11</Parameters_gap-open>
      <Parameters_gap-extend>1</Parameters_gap-extend>
      <Parameters_filter>F</Parameters_filter>
    </Parameters>
  </BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
  <Iteration_iter-num>1</Iteration_iter-num>
  <Iteration_query-ID>Query_1</Iteration_query-ID>
  <Iteration_query-def>seq1</Iteration_query-def>
  <Iteration_query-len>881</Iteration_query-len>
<Iteration_hits>
<Hit>
  <Hit_num>1</Hit_num>
  <Hit_id>gnl|BL_ORD_ID|2</Hit_id>
  <Hit_def>seq3</Hit_def>

test/old-blast/report.blastp.xml  view on Meta::CPAN

      <Statistics_db-num>88</Statistics_db-num>
      <Statistics_db-len>70474</Statistics_db-len>
      <Statistics_hsp-len>70</Statistics_hsp-len>
      <Statistics_eff-space>34150734</Statistics_eff-space>
      <Statistics_kappa>0.041</Statistics_kappa>
      <Statistics_lambda>0.267</Statistics_lambda>
      <Statistics_entropy>0.14</Statistics_entropy>
    </Statistics>
  </Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>

test/report.blastp.xml  view on Meta::CPAN

  <BlastOutput_query-len>881</BlastOutput_query-len>
  <BlastOutput_param>
    <Parameters>
      <Parameters_matrix>BLOSUM62</Parameters_matrix>
      <Parameters_expect>1e-10</Parameters_expect>
      <Parameters_gap-open>11</Parameters_gap-open>
      <Parameters_gap-extend>1</Parameters_gap-extend>
      <Parameters_filter>F</Parameters_filter>
    </Parameters>
  </BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
  <Iteration_iter-num>1</Iteration_iter-num>
  <Iteration_query-ID>Query_1</Iteration_query-ID>
  <Iteration_query-def>seq1</Iteration_query-def>
  <Iteration_query-len>881</Iteration_query-len>
<Iteration_hits>
<Hit>
  <Hit_num>1</Hit_num>
  <Hit_id>seq3</Hit_id>
  <Hit_def>No definition line</Hit_def>

test/report.blastp.xml  view on Meta::CPAN

      <Statistics_db-num>88</Statistics_db-num>
      <Statistics_db-len>70474</Statistics_db-len>
      <Statistics_hsp-len>70</Statistics_hsp-len>
      <Statistics_eff-space>34150734</Statistics_eff-space>
      <Statistics_kappa>0.041</Statistics_kappa>
      <Statistics_lambda>0.267</Statistics_lambda>
      <Statistics_entropy>0.14</Statistics_entropy>
    </Statistics>
  </Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>