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hmmer.t: Added tests to document "$hit->bits"
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and "$hsp->bits" returning value 0
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@fjossandon
fjossandon committed Jul 31, 2014
1 parent e51875b commit 8e5cd1b
Showing 1 changed file with 27 additions and 2 deletions.
29 changes: 27 additions & 2 deletions t/SearchIO/hmmer.t
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Expand Up @@ -7,7 +7,7 @@ BEGIN {
use lib '.'; use lib '.';
use Bio::Root::Test; use Bio::Root::Test;


test_begin( -tests => 773 ); test_begin( -tests => 798 );


use_ok('Bio::SearchIO'); use_ok('Bio::SearchIO');
} }
Expand Down Expand Up @@ -46,6 +46,7 @@ while ( $result = $searchio->next_result ) {
'Check for hit description' 'Check for hit description'
); );
is( $hit->raw_score, 146.1, 'Check hit raw_score' ); is( $hit->raw_score, 146.1, 'Check hit raw_score' );
is( $hit->bits, 0, 'Check hit bits (0)' );
float_is( $hit->significance, 6.3e-40, 'Check hit significance' ); float_is( $hit->significance, 6.3e-40, 'Check hit significance' );
is( $hit->num_hsps, 1, 'Check num_hsps' ); is( $hit->num_hsps, 1, 'Check num_hsps' );


Expand Down Expand Up @@ -75,6 +76,7 @@ while ( $result = $searchio->next_result ) {
is( $hsp->query->start, 33, 'Check for query alifrom value' ); is( $hsp->query->start, 33, 'Check for query alifrom value' );
is( $hsp->query->end, 103, 'Check for query ali to value' ); is( $hsp->query->end, 103, 'Check for query ali to value' );
is( $hsp->score, 71.2, 'Check for hsp score' ); is( $hsp->score, 71.2, 'Check for hsp score' );
is( $hsp->bits, 0, 'Check for hsp bits (0)' );
float_is( $hsp->evalue, 2.2e-17, 'Check for hsp c-Evalue' ); float_is( $hsp->evalue, 2.2e-17, 'Check for hsp c-Evalue' );


is( $hsp->length('query'), 71, 'Check for hsp query length' ); is( $hsp->length('query'), 71, 'Check for hsp query length' );
Expand Down Expand Up @@ -132,6 +134,7 @@ while ( $result = $searchio->next_result ) {
is( $hit->name, 'SEED', 'Check hit name' ); is( $hit->name, 'SEED', 'Check hit name' );
is( $hit->description, '', 'Check for hit description' ); is( $hit->description, '', 'Check for hit description' );
is( $hit->raw_score, 146.1, 'Check hit raw_score' ); is( $hit->raw_score, 146.1, 'Check hit raw_score' );
is( $hit->bits, 0, 'Check hit bits (0)' );
float_is( $hit->significance, 6.3e-040, 'Check hit significance' ); float_is( $hit->significance, 6.3e-040, 'Check hit significance' );
is( $hit->num_hsps, 1, 'Check num_hsps' ); is( $hit->num_hsps, 1, 'Check num_hsps' );


Expand Down Expand Up @@ -161,6 +164,7 @@ while ( $result = $searchio->next_result ) {
is( $hsp->query->start, 124, 'Check for query alifrom value' ); is( $hsp->query->start, 124, 'Check for query alifrom value' );
is( $hsp->query->end, 193, 'Check for query ali to value' ); is( $hsp->query->end, 193, 'Check for query ali to value' );
is( $hsp->score, 75.5, 'Check for hsp score' ); is( $hsp->score, 75.5, 'Check for hsp score' );
is( $hsp->bits, 0, 'Check for hsp bits (0)' );
float_is( $hsp->evalue, 1.1e-18, 'Check for hsp c-Evalue' ); float_is( $hsp->evalue, 1.1e-18, 'Check for hsp c-Evalue' );


is( $hsp->length('query'), 70, 'Check for hsp query length' ); is( $hsp->length('query'), 70, 'Check for hsp query length' );
Expand Down Expand Up @@ -241,6 +245,7 @@ while ( $result = $searchio->next_result ) {
'Check for hit description' 'Check for hit description'
); );
is( $hit->raw_score, 119.7, 'Check hit raw_score' ); is( $hit->raw_score, 119.7, 'Check hit raw_score' );
is( $hit->bits, 0, 'Check hit bits (0)' );
float_is( $hit->significance, 2e-31, 'Check hit significance' ); float_is( $hit->significance, 2e-31, 'Check hit significance' );
is( $hit->num_hsps, 1, 'Check num_hsps' ); is( $hit->num_hsps, 1, 'Check num_hsps' );
is( $hit->length, 0, 'Check hit length' ); is( $hit->length, 0, 'Check hit length' );
Expand All @@ -256,6 +261,7 @@ while ( $result = $searchio->next_result ) {
is( $hsp->query->start, 1, 'Check for query alifrom value' ); is( $hsp->query->start, 1, 'Check for query alifrom value' );
is( $hsp->query->end, 77, 'Check for query ali to value' ); is( $hsp->query->end, 77, 'Check for query ali to value' );
is( $hsp->score, 119.7, 'Check for hsp score' ); is( $hsp->score, 119.7, 'Check for hsp score' );
is( $hsp->bits, 0, 'Check for hsp bits (0)' );
float_is( $hsp->evalue, 2e-31, 'Check for hsp c-Evalue' ); float_is( $hsp->evalue, 2e-31, 'Check for hsp c-Evalue' );


is( $hsp->length('query'), 77, 'Check for hsp query length' ); is( $hsp->length('query'), 77, 'Check for hsp query length' );
Expand Down Expand Up @@ -285,6 +291,7 @@ while ( $result = $searchio->next_result ) {
is( $hsp->query->start, 1, 'Check for query alifrom value' ); is( $hsp->query->start, 1, 'Check for query alifrom value' );
is( $hsp->query->end, 77, 'Check for query ali to value' ); is( $hsp->query->end, 77, 'Check for query ali to value' );
is( $hsp->score, 72.9, 'Check for hsp score' ); is( $hsp->score, 72.9, 'Check for hsp score' );
is( $hsp->bits, 0, 'Check for hsp bits (0)' );
float_is( $hsp->evalue, 2.4e-17, 'Check for hsp c-Evalue' ); float_is( $hsp->evalue, 2.4e-17, 'Check for hsp c-Evalue' );


is( $hsp->length('query'), 77, 'Check for hsp query length' ); is( $hsp->length('query'), 77, 'Check for hsp query length' );
Expand All @@ -310,6 +317,7 @@ while ( $result = $searchio->next_result ) {
is( $hsp->query->start, 1, 'Check for query alifrom value' ); is( $hsp->query->start, 1, 'Check for query alifrom value' );
is( $hsp->query->end, 77, 'Check for query ali to value' ); is( $hsp->query->end, 77, 'Check for query ali to value' );
is( $hsp->score, 3.3, 'Check for hsp score' ); is( $hsp->score, 3.3, 'Check for hsp score' );
is( $hsp->bits, 0, 'Check for hsp bits (0)' );
float_is( $hsp->evalue, 1.9, 'Check for hsp c-Evalue' ); float_is( $hsp->evalue, 1.9, 'Check for hsp c-Evalue' );


is( $hsp->length('query'), 77, 'Check for hsp query length' ); is( $hsp->length('query'), 77, 'Check for hsp query length' );
Expand Down Expand Up @@ -360,6 +368,7 @@ while ( $result = $searchio->next_result ) {
'Check for hit description' 'Check for hit description'
); );
is( $hit->raw_score, -105.2, 'Check hit raw_score' ); is( $hit->raw_score, -105.2, 'Check hit raw_score' );
is( $hit->bits, 0, 'Check hit bits (0)' );
float_is( $hit->significance, 0.0022, 'Check hit significance' ); float_is( $hit->significance, 0.0022, 'Check hit significance' );
is( $hit->num_hsps, 1, 'Check num_hsps' ); is( $hit->num_hsps, 1, 'Check num_hsps' );


Expand Down Expand Up @@ -389,6 +398,7 @@ while ( $result = $searchio->next_result ) {
is( $hsp->query->start, 280, 'Check for query alifrom value' ); is( $hsp->query->start, 280, 'Check for query alifrom value' );
is( $hsp->query->end, 481, 'Check for query ali to value' ); is( $hsp->query->end, 481, 'Check for query ali to value' );
is( $hsp->score, -105.2, 'Check for hsp score' ); is( $hsp->score, -105.2, 'Check for hsp score' );
is( $hsp->bits, 0, 'Check for hsp bits (0)' );
float_is( $hsp->evalue, 0.0022, 'Check for hsp evalue' ); float_is( $hsp->evalue, 0.0022, 'Check for hsp evalue' );


is( $hsp->length('query'), 202, 'Check for hsp query length' ); is( $hsp->length('query'), 202, 'Check for hsp query length' );
Expand Down Expand Up @@ -482,6 +492,7 @@ while ( $result = $searchio->next_result ) {
'Check for hit description' 'Check for hit description'
); );
is( $hit->raw_score, 449.4, 'Check hit raw_score' ); is( $hit->raw_score, 449.4, 'Check hit raw_score' );
is( $hit->bits, 0, 'Check hit bits (0)' );
float_is( $hit->significance, 2e-135, 'Check hit significance' ); float_is( $hit->significance, 2e-135, 'Check hit significance' );
is( $hit->num_hsps, 1, 'Check num_hsps' ); is( $hit->num_hsps, 1, 'Check num_hsps' );


Expand Down Expand Up @@ -511,6 +522,7 @@ while ( $result = $searchio->next_result ) {
is( $hsp->query->start, 1, 'Check for query alifrom value' ); is( $hsp->query->start, 1, 'Check for query alifrom value' );
is( $hsp->query->end, 337, 'Check for query ali to value' ); is( $hsp->query->end, 337, 'Check for query ali to value' );
is( $hsp->score, 449.4, 'Check for hsp score' ); is( $hsp->score, 449.4, 'Check for hsp score' );
is( $hsp->bits, 0, 'Check for hsp bits (0)' );
float_is( $hsp->evalue, 2e-135, 'Check for hsp evalue' ); float_is( $hsp->evalue, 2e-135, 'Check for hsp evalue' );


is( $hsp->length('query'), 337, 'Check for hsp query length' ); is( $hsp->length('query'), 337, 'Check for hsp query length' );
Expand Down Expand Up @@ -559,6 +571,7 @@ while ( $result = $searchio->next_result ) {
is( $hit->name, 'CATL_HUMAN', 'Check hit name' ); is( $hit->name, 'CATL_HUMAN', 'Check hit name' );
is( $hit->description, '', 'Check for hit description' ); is( $hit->description, '', 'Check for hit description' );
is( $hit->raw_score, 444.5, 'Check hit raw_score' ); is( $hit->raw_score, 444.5, 'Check hit raw_score' );
is( $hit->bits, 0, 'Check hit bits (0)' );
float_is( $hit->significance, 6.1e-134, 'Check hit significance' ); float_is( $hit->significance, 6.1e-134, 'Check hit significance' );
} }


Expand Down Expand Up @@ -641,6 +654,7 @@ while ( $result = $searchio->next_result ) {
'Check for hit description' 'Check for hit description'
); );
is( $hit->raw_score, 105.2, 'Check hit raw_score' ); is( $hit->raw_score, 105.2, 'Check hit raw_score' );
is( $hit->bits, 0, 'Check hit bits (0)' );
float_is( $hit->significance, 6e-30, 'Check hit significance' ); float_is( $hit->significance, 6e-30, 'Check hit significance' );
is( $hit->num_hsps, 1, 'Check num_hsps' ); is( $hit->num_hsps, 1, 'Check num_hsps' );


Expand All @@ -661,6 +675,7 @@ while ( $result = $searchio->next_result ) {
is( $hsp->query->start, 2, 'Check for query alifrom value' ); is( $hsp->query->start, 2, 'Check for query alifrom value' );
is( $hsp->query->end, 173, 'Check for query ali to value' ); is( $hsp->query->end, 173, 'Check for query ali to value' );
is( $hsp->score, '105.0', 'Check for hsp score' ); is( $hsp->score, '105.0', 'Check for hsp score' );
is( $hsp->bits, 0, 'Check for hsp bits (0)' );
float_is( $hsp->evalue, 1.5e-33, 'Check for hsp c-Evalue' ); float_is( $hsp->evalue, 1.5e-33, 'Check for hsp c-Evalue' );


is( $hsp->length('query'), 172, 'Check for hsp query length' ); is( $hsp->length('query'), 172, 'Check for hsp query length' );
Expand Down Expand Up @@ -746,6 +761,7 @@ while ( $result = $searchio->next_result ) {
is( $hsp->query->start, 335, 'Check for query alifrom value' ); is( $hsp->query->start, 335, 'Check for query alifrom value' );
is( $hsp->query->end, 369, 'Check for query ali to value' ); is( $hsp->query->end, 369, 'Check for query ali to value' );
is( $hsp->score, 18.9, 'Check for hsp score' ); is( $hsp->score, 18.9, 'Check for hsp score' );
is( $hsp->bits, 0, 'Check for hsp bits (0)' );
float_is( $hsp->evalue, 8.9e-08, 'Check for hsp c-Evalue' ); float_is( $hsp->evalue, 8.9e-08, 'Check for hsp c-Evalue' );
} }
} }
Expand All @@ -766,7 +782,8 @@ while ( $result = $searchio->next_result ) {
is( $hsp->query->start, 335, 'Check for query alifrom value' ); is( $hsp->query->start, 335, 'Check for query alifrom value' );
is( $hsp->query->end, 369, 'Check for query ali to value' ); is( $hsp->query->end, 369, 'Check for query ali to value' );
is( $hsp->score, 18.8, 'Check for hsp score' ); is( $hsp->score, 18.8, 'Check for hsp score' );
float_is( $hsp->evalue, 9e-08, 'Check for hsp c-Evalue' ); is( $hsp->bits, 0, 'Check for hsp bits (0)' );
float_is( $hsp->evalue, 9e-08, 'Check for hsp c-Evalue' );
} }
} }
} }
Expand Down Expand Up @@ -857,6 +874,7 @@ while ( $result = $searchio->next_result ) {
'Check for hit description' 'Check for hit description'
); );
is( $hit->raw_score, -17.8, 'Check hit raw_score' ); is( $hit->raw_score, -17.8, 'Check hit raw_score' );
is( $hit->bits, 0, 'Check hit bits (0)' );
float_is( $hit->significance, 3, 'Check hit significance' ); float_is( $hit->significance, 3, 'Check hit significance' );
is( $hit->num_hsps, 5, 'Check num_hsps' ); is( $hit->num_hsps, 5, 'Check num_hsps' );


Expand All @@ -872,6 +890,7 @@ while ( $result = $searchio->next_result ) {
is( $hsp->query->start, 34, 'Check for query hmmfrom value' ); is( $hsp->query->start, 34, 'Check for query hmmfrom value' );
is( $hsp->query->end, 40, 'Check for query hmm to value' ); is( $hsp->query->end, 40, 'Check for query hmm to value' );
is( $hsp->score, -4.3, 'Check for hsp score' ); is( $hsp->score, -4.3, 'Check for hsp score' );
is( $hsp->bits, 0, 'Check for hsp bits (0)' );
float_is( $hsp->evalue, 1, 'Check for hsp c-Evalue' ); float_is( $hsp->evalue, 1, 'Check for hsp c-Evalue' );


is( $hsp->length('query'), 7, 'Check for hsp query length' ); is( $hsp->length('query'), 7, 'Check for hsp query length' );
Expand Down Expand Up @@ -952,6 +971,7 @@ while ( $result = $searchio->next_result ) {
'Check for hit description' 'Check for hit description'
); );
is( $hit->raw_score, 616.9, 'Check hit raw_score' ); is( $hit->raw_score, 616.9, 'Check hit raw_score' );
is( $hit->bits, 0, 'Check hit bits (0)' );
float_is( $hit->significance, 9.3e-189, 'Check hit significance' ); float_is( $hit->significance, 9.3e-189, 'Check hit significance' );
is( $hit->num_hsps, 1, 'Check num_hsps' ); is( $hit->num_hsps, 1, 'Check num_hsps' );


Expand All @@ -972,6 +992,7 @@ while ( $result = $searchio->next_result ) {
is( $hsp->query->start, 71, 'Check for query hmmfrom value' ); is( $hsp->query->start, 71, 'Check for query hmmfrom value' );
is( $hsp->query->end, 1021, 'Check for query hmm to value' ); is( $hsp->query->end, 1021, 'Check for query hmm to value' );
is( $hsp->score, 616.6, 'Check for hsp score' ); is( $hsp->score, 616.6, 'Check for hsp score' );
is( $hsp->bits, 0, 'Check for hsp bits (0)' );
float_is( $hsp->evalue, 3.9e-189, 'Check for hsp c-Evalue' ); float_is( $hsp->evalue, 3.9e-189, 'Check for hsp c-Evalue' );


is( $hsp->length('query'), 951, 'Check for hsp query length' ); is( $hsp->length('query'), 951, 'Check for hsp query length' );
Expand Down Expand Up @@ -1387,6 +1408,7 @@ is( $result->num_hits(), 2, 'Check num_hits' );
is( $hit->name, 'seq1', 'Check nhmmer hit name' ); is( $hit->name, 'seq1', 'Check nhmmer hit name' );
is( $hit->description, 'Description of seq1', 'Check nhmmer hit description' ); is( $hit->description, 'Description of seq1', 'Check nhmmer hit description' );
is( $hit->score, 148.2, 'Check nhmmer hit score' ); is( $hit->score, 148.2, 'Check nhmmer hit score' );
is( $hit->bits, 0, 'Check nhmmer hit bits (0)' );
float_is( $hit->significance, 3.2e-48, 'Check nhmmer hit significance' ); float_is( $hit->significance, 3.2e-48, 'Check nhmmer hit significance' );
is( $hit->num_hsps, 1, 'Check num_hsps' ); is( $hit->num_hsps, 1, 'Check num_hsps' );


Expand All @@ -1409,6 +1431,7 @@ is( $result->num_hits(), 2, 'Check num_hits' );
is( $hsp->strand('hit'), 1, 'Check nhmmer hsp hit strand' ); is( $hsp->strand('hit'), 1, 'Check nhmmer hsp hit strand' );
is( $hsp->strand('query'), 1, 'Check nhmmer hsp query strand' ); is( $hsp->strand('query'), 1, 'Check nhmmer hsp query strand' );
is( $hsp->score, 148.2, 'Check nhmmer hsp score' ); is( $hsp->score, 148.2, 'Check nhmmer hsp score' );
is( $hsp->bits, 0, 'Check nhmmer hsp bits (0)' );
float_is( $hsp->significance, 3.2e-48, 'Check nhmmer hsp evalue' ); float_is( $hsp->significance, 3.2e-48, 'Check nhmmer hsp evalue' );


is( $hsp->length('query'), 154, 'Check for hsp query length' ); is( $hsp->length('query'), 154, 'Check for hsp query length' );
Expand Down Expand Up @@ -1468,6 +1491,7 @@ is( $result->num_hits(), 2, 'Check num_hits' );
is( $hit->name, 'seq2', 'Check nhmmer hit name' ); is( $hit->name, 'seq2', 'Check nhmmer hit name' );
is( $hit->description, 'Description of seq2', 'Check nhmmer hit description' ); is( $hit->description, 'Description of seq2', 'Check nhmmer hit description' );
is( $hit->score, 38.6, 'Check nhmmer hit score' ); is( $hit->score, 38.6, 'Check nhmmer hit score' );
is( $hit->bits, 0, 'Check nhmmer hit bits (0)' );
float_is( $hit->significance, 3.9e-15, 'Check nhmmer hit significance' ); float_is( $hit->significance, 3.9e-15, 'Check nhmmer hit significance' );
is( $hit->length, 60, 'Check nhmmer hit length' ); is( $hit->length, 60, 'Check nhmmer hit length' );


Expand All @@ -1482,6 +1506,7 @@ is( $result->num_hits(), 2, 'Check num_hits' );
is( $hsp->strand('hit'), -1, 'Check nhmmer hsp hit strand' ); is( $hsp->strand('hit'), -1, 'Check nhmmer hsp hit strand' );
is( $hsp->strand('query'), 1, 'Check nhmmer hsp query strand' ); is( $hsp->strand('query'), 1, 'Check nhmmer hsp query strand' );
is( $hsp->score, 38.6, 'Check nhmmer hsp score' ); is( $hsp->score, 38.6, 'Check nhmmer hsp score' );
is( $hsp->bits, 0, 'Check nhmmer hsp bits (0)' );
float_is( $hsp->significance, 3.9e-15, 'Check nhmmer hsp evalue' ); float_is( $hsp->significance, 3.9e-15, 'Check nhmmer hsp evalue' );


is( $hsp->length('query'), 59, 'Check for hsp query length' ); is( $hsp->length('query'), 59, 'Check for hsp query length' );
Expand Down

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