Class FeatureLocation

Specify the start, end, strand etc of a sequence feature.

start and end arguments specify the values where the feature begins
and ends. These can either by any of the *Position objects that
inherit from AbstractPosition, or can just be integers specifying the
position. In the case of integers, the values are assumed to be
exact and are converted in ExactPosition arguments. This is meant
to make it easy to deal with non-fuzzy ends.

i.e. Short form:

>>> from Bio.SeqFeature import FeatureLocation
>>> loc = FeatureLocation(5, 10, strand=-1)
>>> print loc
[5:10](-)

Explicit form:

>>> from Bio.SeqFeature import FeatureLocation, ExactPosition
>>> loc = FeatureLocation(ExactPosition(5), ExactPosition(10), strand=-1)
>>> print loc
[5:10](-)

Other fuzzy positions are used similarly,

>>> from Bio.SeqFeature import FeatureLocation
>>> from Bio.SeqFeature import BeforePosition, AfterPosition
>>> loc2 = FeatureLocation(BeforePosition(5), AfterPosition(10), strand=-1)
>>> print loc2
[<5:>10](-)

For nucleotide features you will also want to specify the strand,
use 1 for the forward (plus) strand, -1 for the reverse (negative)
strand, 0 for stranded but strand unknown (? in GFF3), or None for
when the strand does not apply (dot in GFF3), e.g. features on
proteins.

>>> loc = FeatureLocation(5, 10, strand=+1)
>>> print loc
[5:10](+)
>>> print loc.strand
1

Normally feature locations are given relative to the parent
sequence you are working with, but an explicit accession can
be given with the optional ref and db_ref strings:

>>> loc = FeatureLocation(105172, 108462, ref="AL391218.9", strand=1)
>>> print loc
AL391218.9[105172:108462](+)
>>> print loc.ref
AL391218.9

Overrides: object.__init__

Returns a representation of the location (with python counting).

For the simple case this uses the python splicing syntax, [122:150]
(zero based counting) which GenBank would call 123..150 (one based
counting).

Overrides: object.__str__

A string representation of the location for debugging.

Overrides: object.__repr__

Returns True regardless of the length of the feature.

This behaviour is for backwards compatibility, since until the
__len__ method was added, a FeatureLocation always evaluated as True.

Note that in comparison, Seq objects, strings, lists, etc, will all
evaluate to False if they have length zero.

WARNING: The FeatureLocation may in future evaluate to False when its
length is zero (in order to better match normal python behaviour)!

Returns the length of the region described by the FeatureLocation.

Note that extra care may be needed for fuzzy locations, e.g.

>>> from Bio.SeqFeature import FeatureLocation
>>> from Bio.SeqFeature import BeforePosition, AfterPosition
>>> loc = FeatureLocation(BeforePosition(5),AfterPosition(10))
>>> len(loc)
5

Check if an integer position is within the FeatureLocation.

Note that extra care may be needed for fuzzy locations, e.g.

>>> from Bio.SeqFeature import FeatureLocation
>>> from Bio.SeqFeature import BeforePosition, AfterPosition
>>> loc = FeatureLocation(BeforePosition(5),AfterPosition(10))
>>> len(loc)
5
>>> [i for i in range(15) if i in loc]
[5, 6, 7, 8, 9]

Iterate over the parent positions within the FeatureLocation.

>>> from Bio.SeqFeature import FeatureLocation
>>> from Bio.SeqFeature import BeforePosition, AfterPosition
>>> loc = FeatureLocation(BeforePosition(5),AfterPosition(10))
>>> len(loc)
5
>>> for i in loc: print i
5
6
7
8
9
>>> list(loc)
[5, 6, 7, 8, 9]
>>> [i for i in range(15) if i in loc]
[5, 6, 7, 8, 9]

Note this is strand aware:

>>> loc = FeatureLocation(BeforePosition(5), AfterPosition(10), strand = -1)
>>> list(loc)
[9, 8, 7, 6, 5]

strand

Strand of the location (+1, -1, 0 or None).

Get Method:

_get_strand(self)

Set Method:

_set_strand(self, value)

start

Start location (integer like, possibly a fuzzy position, read only).

Get Method:

unreachable.start(self) - Start location (integer like, possibly a fuzzy position, read only).

end

End location (integer like, possibly a fuzzy position, read only).

Get Method:

unreachable.end(self) - End location (integer like, possibly a fuzzy position, read only).

nofuzzy_start

Start position (integer, approximated if fuzzy, read only) (OBSOLETE).

This is now a alias for int(feature.start), which should be
used in preference -- unless you are trying to support old
versions of Biopython.

Get Method:

unreachable.nofuzzy_start(self) - Start position (integer, approximated if fuzzy, read only) (OBSOLETE).

nofuzzy_end

End position (integer, approximated if fuzzy, read only) (OBSOLETE).

This is now a alias for int(feature.end), which should be
used in preference -- unless you are trying to support old
versions of Biopython.  

Get Method:

unreachable.nofuzzy_end(self) - End position (integer, approximated if fuzzy, read only) (OBSOLETE).