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Class: SeqFeature Bio/SeqFeature.py

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.

Methods   
__init__
__str__
  __init__ 
__init__ (
        self,
        location=None,
        type='',
        location_operator='',
        strand=None,
        id="<unknown id>",
        qualifiers={},
        sub_features=[],
        ref=None,
        ref_db=None,
        )

Initialize a SeqFeature on a Sequence.

  __str__ 
__str__ ( self )

Make it easier to debug features.


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This document was automatically generated on Mon Jul 1 12:02:43 2002 by HappyDoc version 2.0.1