/ 
Bio-DOOP-DOOP-0.24
River stage zero No dependents
/ Bio::DOOP::SequenceFeature

NAME

Bio::DOOP::SequenceFeature - Object for the sequence features

VERSION

Version 0.08

SYNOPSIS

DESCRIPTION

This object gives access to the sequence features ( conserved motif, repeat, CpG island,
TFBS and TSS annotation ).

AUTHOR

Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary

METHODS

new

 $seqfeat = Bio::DOOP::SequenceFeature->new($db,"112");

 You can create the object with the new method.
 The arguments are the following : Bio::DOOP::DBSQL object, sequence_feature_primary_id

get_id

Returns the primary ID of the feature. This is the internal ID from the MySQL database.

get_score

Returns the score of the feature. We don't really need this now.

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.
Return type: string

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

$motif = $seqfeat->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".