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t/SearchIO/blastxml.t  view on Meta::CPAN

    is($hsp->query->start, 1);
    is($hsp->query->end,348);
    is($hsp->hit->start, 1);
    is($hsp->hit->end, 348);
    is($hsp->query->frame,0);
    is($hsp->hit->frame,0);

    # PSIBLAST XML parsing

    $searchio = Bio::SearchIO->new('-tempfile' => 1,
           '-format' => 'blastxml',
           '-file'   => test_input_file('psiblast.xml'),
           '-blasttype' => 'psiblast');

    $result = $searchio->next_result;
    is($searchio->result_count, 1);
    is($result->database_name, 'AL591824.faa');
    is($result->algorithm, 'BLASTP');
    like($result->algorithm_version, qr/2\.2\.16/);
    is($result->query_name, 'gi|1373160|gb|AAB57770.1|');
    is($result->query_accession, 'AAB57770.1');
    is($result->query_gi, '1373160');
    is($result->query_length, 173);

    # check parameters
    is($result->available_parameters, 6);
    is($result->get_parameter('matrix'), 'BLOSUM62');
    float_is($result->get_parameter('expect'), 10);
    is($result->get_parameter('include'), 0.002);
    is($result->get_parameter('match'), undef);   # not set
    is($result->get_parameter('mismatch'), undef);# not set
    is($result->get_parameter('gapopen'), 11);
    is($result->get_parameter('gapext'), 1);
    is($result->get_parameter('filter'), 'F');

    # check statistics
    is($result->available_statistics, 5);
    is($result->database_entries, 2846);
    is($result->database_letters, 870878);
    is($result->get_statistic('hsplength'), 75);
    float_is($result->get_statistic('effectivespace'), 6.44279e+07);
    is($result->get_statistic('lambda'), 0.267);
    is($result->get_statistic('kappa'), 0.0475563);
    is($result->get_statistic('entropy'), 0.14);

    my $iter_count = 0;
    my @valid_hit_data = ( [ 'gi|16411294|emb|CAC99918.1|', 183, 'CAC99918', 16411294, '4.5377e-56', 209.92],
                   [ 'gi|16409584|emb|CAD00746.1|', 648, 'CAD00746', 16409584, '0.000286309', 37.7354],
                   [ 'gi|16411285|emb|CAC99909.1|', 209, 'CAC99909', 16411285, '0.107059', 29.261]);
    my @valid_iter_data = ( [ 16, 16, 0, 2, 14, 0, 0, 0, 0],
                [ 16, 8, 8, 0, 8, 0, 2, 0, 6]);

    while (my $iter = $result->next_iteration) {
        $iter_count++;
        my $di = shift @valid_iter_data;
        is($iter->number, $iter_count);
        is($iter->num_hits, shift @$di);
        is($iter->num_hits_new, shift @$di);
        is($iter->num_hits_old, shift @$di);
        is(scalar($iter->newhits_below_threshold), shift @$di);
        is(scalar($iter->newhits_not_below_threshold), shift @$di);
        is(scalar($iter->newhits_unclassified), shift @$di);
        is(scalar($iter->oldhits_below_threshold), shift @$di);
        is(scalar($iter->oldhits_newly_below_threshold), shift @$di);
        is(scalar($iter->oldhits_not_below_threshold), shift @$di);
        my $hit_count = 0;
        if ($iter_count == 1) {
            while( my $hit = $result->next_hit ) {
                my $d = shift @valid_hit_data;
                is($hit->name, shift @$d);
                is($hit->length, shift @$d);
                is($hit->accession, shift @$d);
                is($hit->ncbi_gi, shift @$d);
                float_is($hit->significance, shift @$d);
                is($hit->bits, shift @$d );
                if( $hit_count == 1 ) {
                    my $hsps_left = 1;
                    while( my $hsp = $hit->next_hsp ){
                        is($hsp->query->start, 4);
                        is($hsp->query->end, 155);
                        is($hsp->hit->start, 475);
                        is($hsp->hit->end, 617);
                        is($hsp->length('total'), 153);
                        is($hsp->start('hit'), $hsp->hit->start);
                        is($hsp->end('query'), $hsp->query->end);
                        is($hsp->strand('sbjct'), $hsp->subject->strand);# alias for hit
                        float_is($hsp->evalue, 0.000286309);
                        is($hsp->score, 86);
                        is($hsp->bits, 37.7354);
                        is(sprintf("%.1f",$hsp->percent_identity), 20.9);
                        is(sprintf("%.4f",$hsp->frac_identical('query')), 0.2105);
                        is(sprintf("%.3f",$hsp->frac_identical('hit')), 0.224);
                        is($hsp->gaps('total'), 11);
                        $hsps_left--;
                    }
                    is($hsps_left, 0);
                }
                last if( $hit_count++ > @valid_hit_data );
            }
        }
    }
    is(@valid_hit_data, 0);
    is(@valid_iter_data, 0);
    is($iter_count, 2);

    $result = $searchio->next_result;
    is($searchio->result_count, 2);
    is($result->database_name, 'AL591824.faa');
    is($result->algorithm, 'BLASTP');
    like($result->algorithm_version, qr/2\.2\.16/);
    is($result->query_name, 'gi|154350371|gb|ABS72450.1|');
    is($result->query_accession, 'ABS72450.1');
    is($result->query_gi, '154350371');
    is($result->query_length, 378);

    # check parameters
    is($result->available_parameters, 6);
    is($result->get_parameter('matrix'), 'BLOSUM62');
    float_is($result->get_parameter('expect'), 10);
    is($result->get_parameter('include'), 0.002);
    is($result->get_parameter('match'), undef);   # not set
    is($result->get_parameter('mismatch'), undef);# not set
    is($result->get_parameter('gapopen'), 11);
    is($result->get_parameter('gapext'), 1);
    is($result->get_parameter('filter'), 'F');

    # check statistics
    is($result->available_statistics, 5);
    is($result->database_entries, 2846);
    is($result->database_letters, 870878);
    is($result->get_statistic('hsplength'), 82);
    float_is($result->get_statistic('effectivespace'), 1.88702e+08);
    is($result->get_statistic('lambda'), 0.267);
    is($result->get_statistic('kappa'), 0.0450367);
    is($result->get_statistic('entropy'), 0.14);

    $iter_count = 0;

    @valid_hit_data = ( [ 'gi|16409361|emb|CAC98217.1|', 381, 'CAC98217', 16409361, '5.57178e-119', 420.239],
                   [ 'gi|16409959|emb|CAC98662.1|', 776, 'CAC98662', 16409959, '0.0242028', 32.7278],
                   [ 'gi|16410942|emb|CAC99591.1|', 382, 'CAC99591', 16410942, '0.340848', 28.8758]);
    @valid_iter_data = ( [ 11, 11, 0, 1, 10, 0, 0, 0, 0],
                [ 19, 11, 8, 0, 11, 0, 1, 0, 7]);

    while (my $iter = $result->next_iteration) {
        $iter_count++;
        my $di = shift @valid_iter_data;
        is($iter->number, $iter_count);
        is($iter->num_hits, shift @$di);
        is($iter->num_hits_new, shift @$di);
        is($iter->num_hits_old, shift @$di);
        is(scalar($iter->newhits_below_threshold), shift @$di);
        is(scalar($iter->newhits_not_below_threshold), shift @$di);
        is(scalar($iter->newhits_unclassified), shift @$di);
        is(scalar($iter->oldhits_below_threshold), shift @$di);
        is(scalar($iter->oldhits_newly_below_threshold), shift @$di);
        is(scalar($iter->oldhits_not_below_threshold), shift @$di);
        my $hit_count = 0;
        if ($iter_count == 1) {
            while( my $hit = $result->next_hit ) {
                my $d = shift @valid_hit_data;
                is($hit->name, shift @$d);
                is($hit->length, shift @$d);
                is($hit->accession, shift @$d);
                is($hit->ncbi_gi, shift @$d);
                float_is($hit->significance, shift @$d);
                is($hit->bits, shift @$d );
                if( $hit_count == 1 ) {
                    my $hsps_left = 1;
                    while( my $hsp = $hit->next_hsp ){
                        is($hsp->query->start, 63);
                        is($hsp->query->end, 181);
                        is($hsp->hit->start, 304);
                        is($hsp->hit->end, 432);
                        is($hsp->length('total'), 129);
                        is($hsp->start('hit'), $hsp->hit->start);
                        is($hsp->end('query'), $hsp->query->end);
                        is($hsp->strand('sbjct'), $hsp->subject->strand);# alias for hit
                        float_is($hsp->evalue, 0.0242028);
                        is($hsp->score, 73);
                        is($hsp->bits, 32.7278);
                        is(sprintf("%.1f",$hsp->percent_identity), '24.0');
                        is(sprintf("%.4f",$hsp->frac_identical('query')), '0.2605');
                        is(sprintf("%.3f",$hsp->frac_identical('hit')), '0.240');
                        is($hsp->gaps, 10);
                        $hsps_left--;
                    }
                    is($hsps_left, 0);
                }
                last if( $hit_count++ > @valid_hit_data );
            }
        }
    }
    is(@valid_hit_data, 0);
    is(@valid_iter_data, 0);
    is($iter_count, 2);
}