skbio.metadata.Interval#

class skbio.metadata.Interval(interval_metadata, bounds, fuzzy=None, metadata=None)[source]#

Stores the bounds and metadata of an interval feature.

This class stores an interval feature. An interval feature is defined as a sub-region of a biological sequence or sequence alignment that is a functional entity, e.g., a gene, a riboswitch, an exon, etc. It can span a single contiguous region or multiple non-contiguous regions (e.g. multiple exons in a transcript, or multiple genes in an operon).

Parameters:

interval_metadataobject: A reference to the IntervalMetadata object that this Interval object is associated to.
boundsiterable of tuple of int: Tuples representing start and end coordinates. It is zero-based numbering. It is always inclusive on start bound and exclusive on end bound.
fuzzyiterable of tuple of bool, optional: Tuples representing the fuzziness of each bound coordinates. If this isn’t specified, then the fuzziness of all bound coordinates are False. If any of the coordinate fuzziness is True, it indicates that the exact bound point of a interval feature is unknown. The bound may begin or end at some points outside the specified coordinates. This accommodates the location format [1] of INSDC.
metadatadict, optional: Dictionary of attributes storing information of the feature such as “strand”, “gene_name”, or “product”.

See also

skbio.metadata.IntervalMetadata

Notes

While the construction of an Interval object automatically add itself to its associated IntervalMetadata object, IntervalMetadata.add is the typical/easier way to create and add it to IntervalMetadata.

References

[1]

ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html#3.4.3

Examples

Hypothetically, let’s say we have a gene called “genA” with 10 nt as shown in the following diagram. The second row represents the two exons (indicated by “=”) on this gene:

TGGATTCTGC
-====--==-
0123456789

We can create an Interval object to represent the exons of the gene:

>>> from skbio.metadata import Interval, IntervalMetadata
>>> interval_metadata = IntervalMetadata(10)

Remember the coordinates are inclusive in lower bound and exclusive on upper bound:

>>> gene = Interval(interval_metadata,
...                 bounds=[(1, 5), (7, 9)],
...                 metadata={'name': 'genA'})
>>> gene    
Interval(interval_metadata=..., bounds=[(1, 5), (7, 9)], fuzzy=[(False, False), (False, False)], metadata={'name': 'genA'})

Attributes

`bounds`	The coordinates of the interval feature.
`dropped`	Boolean value indicating if the `Interval` object is dropped.
`fuzzy`	The openness of each coordinate.
`metadata`	The metadata of the interval feature.

Methods

drop()

Drop this Interval object from interval metadata it links to.

Special methods

`__eq__`(other)	Test if this `Interval` object is equal to another.
`__ne__`(other)	Test if this `Interval` object is not equal to another.

Special methods (inherited)

`__ge__`(value, /)	Return self>=value.
`__getstate__`(/)	Helper for pickle.
`__gt__`(value, /)	Return self>value.
`__le__`(value, /)	Return self<=value.
`__lt__`(value, /)	Return self<value.
`__str__`(/)	Return str(self).

Details

bounds#

The coordinates of the interval feature.

It should be a list of tuples of int pair. Each tuple stores the start and end coordinates of a span of the interval feature. The coordinates are zero-based. They are inclusive on the start and exclusive on the end.

dropped#

Boolean value indicating if the Interval object is dropped.

If it is dropped, it means it is not associated with IntervalMetadata object any more.