Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity
of two sequences.
$sim_pair = Bio::SeqFeature::SimilarityPair->from_searchResult($blastHit);
$sim = $sim_pair->query(); # a Bio::SeqFeature::Similarity object - the query
$sim = $sim_pair->hit(); # dto - the hit.
# some properties for the similarity pair
$expect = $sim_pair->significance();
$score = $sim_pair->score();
$bitscore = $sim_pair->bits();
# this will not write the description for the sequence (only its name)
print $sim_pair->query()->gff_string(), "\n";
Lightweight similarity search result as a pair of Similarity features. This
class inherits off Bio::SeqFeature::FeaturePair and therefore implements
Bio::SeqFeatureI, whereas the two features of the pair are descendants of
Bio::SeqFeature::Generic, with better support for representing similarity
search results in a cleaner way.
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The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
Title : new
Usage : my $similarityPair = Bio::SeqFeature::SimilarityPair->new
(-hit => $hit,
-query => $query,
-source => 'blastp');
Function: Initializes a new SimilarityPair object
Returns : Bio::SeqFeature::SimilarityPair
Args : -query => The query in a Feature pair
-hit => (formerly '-subject') the subject/hit in a Feature pair
Title : query
Usage : $query_feature = $obj->query();
$obj->query($query_feature);
Function: The query object for this similarity pair
Returns : Bio::SeqFeature::Similarity
Args : [optional] Bio::SeqFeature::Similarity
See Bio::SeqFeature::Similarity, Bio::SeqFeature::FeaturePair
Title : subject
Usage : $sbjct_feature = $obj->subject();
$obj->subject($sbjct_feature);
Function: Get/Set Subject for a SimilarityPair
Returns : Bio::SeqFeature::Similarity
Args : [optional] Bio::SeqFeature::Similarity
Notes : Deprecated. Use the method 'hit' instead
Title : hit
Usage : $sbjct_feature = $obj->hit();
$obj->hit($sbjct_feature);
Function: Get/Set Hit for a SimilarityPair
Returns : Bio::SeqFeature::Similarity
Args : [optional] Bio::SeqFeature::Similarity
Title : source_tag
Usage : $source = $obj->source_tag(); # i.e., program
$obj->source_tag($evalue);
Function: Gets the source tag (program name typically) for a feature
Returns : string
Args : [optional] string
Title : significance
Usage : $evalue = $obj->significance();
$obj->significance($evalue);
Function:
Returns :
Args :
Title : score
Usage : $score = $obj->score();
$obj->score($value);
Function:
Returns :
Args :
Title : bits
Usage : $bits = $obj->bits();
$obj->bits($value);
Function:
Returns :
Args :