Bio::DOOP::Motif - DOOP database motif object
Version 0.6
use Bio::DOOP::Motif; $db = Bio::DOOP::DBSQL->connect("user","pass","database","somewhere.where.org"); my $motif = Bio::DOOP::Motif->new($db,"160945"); print $motif->seq,":",$motif->start," ",$motif->end,"\n";
This object represents the conserved motifs. You should not use the constructor directly, but sometimes it is useful. In most cases you get this object from other objects.
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
$motif = Bio::DOOP::Motif->new($db,"1234"); You can create the object with the new method. The arguments are the following : Bio::DOOP::DBSQL object, motif_primary_id
$motif_type = $motif->type; Returns the type of the motif. Return type : string
$motif_seq = $motif->seq; Returns the consensus sequence of the motif. Return type : string
$start = $motif->start; Returns the start position of the motif. Return type : string
$end = $motif->end; Returns the end position of the motif. Return type : string;
$length = $motif->length; Returns the length of the motif. Return type : string
$primary_id = $motif->get_id; Returns the primary ID of the motif. This is the internal ID from the MySQL database. Return type : string
$subset_id = $motif->get_subset_id; Returns the motif subset primary id. Return type : string
@feats = @{$motif->get_seqfeats} Returns all the sequence features, associated with the motif. Return type : arrayref, the array containig Bio::DOOP::SequenceFeature objects
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.