NAME¶
Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity
of two sequences.
SYNOPSIS¶
$sim_pair = Bio::SeqFeature::SimilarityPair->from_searchResult($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";
DESCRIPTION¶
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.
FEEDBACK¶
Mailing Lists¶
User feedback is an integral part of the evolution of this and other Bioperl
modules. Send your comments and suggestions preferably to one of the Bioperl
mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support¶
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive
experts will be able look at the problem and quickly address it. Please
include a thorough description of the problem with code and data examples if
at all possible.
Reporting Bugs¶
Report bugs to the Bioperl bug tracking system to help us keep track the bugs
and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Hilmar Lapp¶
Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
new¶
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
query¶
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
subject¶
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
hit¶
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
source_tag¶
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
significance¶
Title : significance
Usage : $evalue = $obj->significance();
$obj->significance($evalue);
Function:
Returns :
Args :
score¶
Title : score
Usage : $score = $obj->score();
$obj->score($value);
Function:
Returns :
Args :
bits¶
Title : bits
Usage : $bits = $obj->bits();
$obj->bits($value);
Function:
Returns :
Args :