NAME

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

VERSION

Version 0.03

DESCRIPTION

  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.

AUTHOR

  Tibor Nagy, Godollo, Hungary

METHODS

new

  $seqfeat = Bio::DOOP::SequenceFeature->new($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.

get_id

  Return the primary id of the features. Use for MySQL queryes

get_score

  Return the score of the feature. I do not know too much about it.

get_start

  Return the start position of the feature.

get_end

  Return the end position of the feature

get_png_topleft

  Return the picture position of the feature. Used by a web code

get_png_topright

  Return the picture position of the feature. Used by a web code

get_png_bottomleft

  Return the picture position of the feature. Used by a web code

get_png_bottomright

  Return the picture position of the feature. Used by a web code

get_seq

  Return the sequence of the feature.

get_type

  Return the type of the feature. (con, ssr, tfbs, rep, cpg, tss)

get_motifid

  Return the motif primary id, if the feature type is con. Else it is NULL

get_tfbsid

  Return the tfbs primary id, if the feature type is tfbs. Else it is NULL

get_cpgid

  Return the cpg primary id, if the feature type is cpg. Else it is NULL

get_repeatid

  Return the repeat primary id, if the feature type is rep. Else it is NULL

get_ssrid

  Return the ssr primary id, if the feature type is ssr. Else it is NULL

get_tssid

  Return the tss primary id, if the feature type is tss. Else it is NULL

get_seqid

  Return the sequence primary id that is contain this feature

get_subsetid

  The get_subsetid method returns the subset primary id of the feature

get_motif

  $motif = $seqfeat->get_motif;
  Return the motif object associated to the feature.
  If the feature type is not con this value is NULL

get_tss_type

  Return the tss type, if the feature is tss.

get_tss_id

  Return the tss id, if the feature is tss.

get_tss_desc

  Return the description of the tss, if the feature is tss

get_tss_xref

  Return the xref of the tss, if the feature is tss

cpanm Bio::DOOP::DOOP

perl -MCPAN -e shell
install Bio::DOOP::DOOP