NAME
Bio::DOOP::SequenceFeature - Object for the sequence features
VERSION
Version 0.10
SYNOPSIS
my $seqfeat = Bio::DOOP::SequenceFeature->new($db,"112");
my $type = $seqfeat->get_type;DESCRIPTION
This object gives access to the sequence features (conserved motif, repeat, CpG island, TFBS and TSS annotation).
AUTHORS
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
METHODS
new
Creates a new sequence feature object from the sequence feature primary id.
Return type: Bio::DOOP::SequenceFeature object
$seqfeat = Bio::DOOP::SequenceFeature->new($db,"112");get_id
Returns the primary ID of the feature. This is the internal ID from the MySQL database.
get_score
This method is not yet implemented.
get_start
Returns the start position of the feature.
get_end
Returns the end position of the feature.
length
Returns the length of the feature.
get_seq
Returns the sequence of the feature.
get_type
Returns the type of the feature. (con, ssr, tfbs, rep, cpg, tss).
con : evolutionary conserved non-coding region ssr : simple sequence repeat tfbs : transcription factor binding site rep : repeat cpg : cpg island tss : transcription start site
get_motifid
Returns the motif primary ID, if the feature type is "con".
get_tfbsid
Returns the tfbs primary ID, if the feature type is "tfbs".
get_cpgid
Returns the cpg primary ID, if the feature type is "cpg".
get_repeatid
Returns the repeat primary ID, if the feature type is "rep".
get_ssrid
Returns the ssr primary ID, if the feature type is "ssr".
get_tssid
Returns the tss primary ID, if the feature type is "tss".
get_seqid
Returns the primary ID of the sequence containing this feature.
get_subsetid
Returns the subset primary ID of the feature, if the feature type is "con".
get_motif
Returns the motif object associated with the feature. If the feature type is not "con" this value is NULL.
get_tss_type
Returns the tss type, if the feature type is "tss".
get_tss_id
Returns the tss id, if the feature type is "tss".
get_tss_desc
Returns the description of the tss, if the feature type is "tss".
get_tss_xref
Returns the xref of the tss, if the feature type is "tss".