Class SeqFeature
Represent a Sequence Feature on an object.
Attributes: o location - the location of the feature on the sequence o
type - the specified type of the feature (ie. CDS, exon, repeat...) o
location_operator - a string specifying how this SeqFeature may be
related to others. For example, in the example GenBank feature shown
below, the location_operator would be "join" o strand - A value
specifying on which strand (of a DNA sequence, for instance) the feature
deals with. 1 indicates the plus strand, -1 indicates the minus strand, 0
indicates both strands, and None indicates that strand doesn't apply (ie.
for proteins) or is not known. o id - A string identifier for the
feature. o ref - A reference to another sequence. This could be an
accession number for some different sequence. o ref_db - A different
database for the reference accession number. o qualifier - A dictionary
of qualifiers on the feature. These are analagous to the qualifiers from
a GenBank feature table. The keys of the dictionary are qualifier names,
the values are the qualifier values. o sub_features - Additional
SeqFeatures which fall under this 'parent' feature. For instance, if we
having something like:
CDS join(1..10,30..40,50..60)
The the top level feature would be a CDS from 1 to 60, and the sub
features would be of 'CDS_join' type and would be from 1 to 10, 30 to 40
and 50 to 60, respectively.
Method Summary |
|
__init__ (self,
location,
type,
location_operator,
strand,
id,
qualifiers,
sub_features,
ref,
ref_db)
Initialize a SeqFeature on a Sequence. |
|
__str__ (self)
Make it easier to debug features. |
__init__(self,
location=None,
type='',
location_operator='',
strand=None,
id='<unknown id>',
qualifiers={},
sub_features=[],
ref=None,
ref_db=None)
(Constructor)
Initialize a SeqFeature on a Sequence.
-
|
__str__(self)
(Informal representation operator)
Make it easier to debug features.
-
|