Tibor Nagy > Bio-DOOP-DOOP-1.02 > Bio::DOOP::Motif

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Bio-DOOP-DOOP-1.02.tar.gz

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Module Version: 0.6   Source   Latest Release: Bio-DOOP-DOOP-1.04

NAME ^

  Bio::DOOP::Motif - DOOP database motif object

VERSION ^

Version 0.6

SYNOPSIS ^

  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";

DESCRIPTION ^

  This object represents the conserved motifs.
  You should not use the constructor directly, but
  sometimes it can be useful. In most cases you
  get this object from other objects.

AUTHORS ^

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

METHODS ^

new

  $motif = Bio::DOOP::Motif->new($db,"1234");
 
  You can create the object with the new method.

  The arguments are the following : Bio::DOOP::DBSQL object, motif_primary_id

type

  $motif_type = $motif->type;

  Returns the type of the motif.

  Return type : string

seq

  $motif_seq = $motif->seq;

  Returns the consensus sequence of the motif.

  Return type : string

start

  $start = $motif->start;

  Returns the start position of the motif.

  Return type : string

end

  $end = $motif->end;

  Returns the end position of the motif.

  Return type : string;

length

  $length = $motif->length;

  Returns the length of the motif.

  Return type : string

get_id

  $primary_id = $motif->get_id;

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

  Return type : string

get_subset_id

  $subset_id = $motif->get_subset_id;

  Returns the motif subset primary id.

  Return type : string

get_seqfeats

  @feats = @{$motif->get_seqfeats}

  Returns all the sequence features, associated with the motif.

  Return type : arrayref, the array containing Bio::DOOP::SequenceFeature objects.
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