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Bio::SeqFeature::SeqFeature Class Reference

List of all members.

Detailed Description

Represent a Sequence Feature on an object.

o location - the location of the feature on the sequence (FeatureLocation)
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 qualifiers - 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
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.

To get the nucleotide sequence for this CDS, you would need to take the
parent sequence and do seq[0:10]+seq[29:40]+seq[49:60] (Python counting).
Things are more complicated with strands and fuzzy positions. To save you
dealing with all these special cases, the SeqFeature provides an extract
method to do this for you.

Definition at line 44 of file SeqFeature.py.

Public Member Functions

def __init__
def __repr__
def __str__
def extract

Public Attributes


Private Member Functions

def _shift

The documentation for this class was generated from the following file:

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