Bio::DOOP::SequenceFeature - Object for the sequence features
This object give access for the sequence features ( motif, repeat, cpg and tss annotaion ). This object also contain some web based code for visualize the feature in picture.
Tibor Nagy, Godollo, Hungary
$seqfeat = Bio::DOOP::SequenceFeature->new($db,"112"); You can create the object with new. The arguments is the following: $db is a Bio::DOOP::DBSQL object, the second argument is a SequenceFeature primary id.
Return the primary id of the features. Use for MySQL queryes
Return the score of the feature. I do not know too much about it.
Return the start position of the feature.
Return the end position of the feature
Return the picture position of the feature. Used by a web code
Return the sequence of the feature.
Return the type of the feature. (con, ssr, tfbs, rep, cpg, tss)
Return the motif primary id, if the feature type is con. Else it is NULL
Return the tfbs primary id, if the feature type is tfbs. Else it is NULL
Return the cpg primary id, if the feature type is cpg. Else it is NULL
Return the repeat primary id, if the feature type is rep. Else it is NULL
Return the ssr primary id, if the feature type is ssr. Else it is NULL
Return the tss primary id, if the feature type is tss. Else it is NULL
Return the sequence primary id that is contain this feature
$motif = $seqfeat->get_motif; Return the motif object associated to the feature. If the feature type is not con this value is NULL
To install Bio::DOOP::DOOP, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::DOOP::DOOP
CPAN shell
perl -MCPAN -e shell install Bio::DOOP::DOOP
For more information on module installation, please visit the detailed CPAN module installation guide.