Yatel Objects

Yatel has a series of classes in the file yatel.dom that serve to abstract the information into data structures that we conceptually use in nw-olap

All classes defined there having behavior like immutable dictionaries and most notably of all is probably dom.Haplotype. So assuming two objects of either class, the following statements are equivalent obj.attribute o obj["attribute"].

Like any dictionary, they have available methods like items(), keys() values() and get(k).

All instances of yatel.dom for being immutable can be used as keys in a dictionary except that the object contains a non hasheable element. Example:

>>> from yatel import dom

>>> hap = dom.Haplotype(1)
>>> data = {hap: 1} # works

>>> hap = dom.Haplotype(2, attr=[1,2,3]) # warning list is unhashable
>>> data = {hap: 1} # works
TypeError: unhashable type: 'list'


  • dom.Haplotype represents a node in a nw-olap and receives at least one parameter (hap_id) others being named optionally. Two haplotypes are equal if they have the same hap_id regardless of other attributes. Another important feature is that attributes with values ​​None are not taken into account and removed.


>>> from yatel import dom
>>> hap0 = dom.Haplotype(1)
>>> hap1 = dom.Haplotype(1, attr="foo", attr2=None)
>>> hap0 == hap1

>>> "attr" in hap0
>>> "attr" in hap1

>>> hap1.attr2 # invalid because is None
AttributeError: 'Haplotype' object has no attribute 'attr2'

>>> hap1.attr
>>> hap1["attr"]
>>hap0.get("wat?", "default")

>>> hash(hap0) == hash(hap1)

>>> id(hap0) == id(hap1)

>>> hap0 is hap1

>>> len(hap0)
>>> len(hap1)

>>> d = {hap0: "foo"}
>>> d[hap1] # remember same hap_id

  >>> hap1 in d and hap0 in d
  • dom.Edge represents an edge in the nw-olap. Receives two parameters in its constructor: The first is the weight of arc (always converted to float) and the second is an iterable with the hap_id of the haplotypes associated. Two edges are equal only if they have the same weight and the same haplotypes connected. Only have two attributes that are the same as the constructor: it’s weight edge.weight and connections in a tuple edge.haps_id
>>> from yatel import dom
>>> edge0 = dom.Edge(1, [1, 2]) # weight 1 and connect haps 1 and 2
>>> edge1 = dom.Edge(1.0, [1, 3]) # weight 1 and connect haps 1 and 3
>>> edge0 == edge1

>>> edge0.haps_id
(1, 2)

>>> d = {edge0: "foo", edge1: "waa"}
>>> d
{<Edge (1.0 (1, 2)) at 0x259a710>: 'foo',
<Edge (1.0 (1, 3)) at 0x259a750>: 'waa'}
  • dom.Fact are the meta data of the analysis of haplotypes. Only their first parameter is required, hap_id of the haplotype to which they belong, and all other named parameters are optional. dom.Fact are equal only if they belong to the same haplotype and possesses the same attributes with the same values. Another important feature is that attributes with values None are not taken into account and removed.
>>> from yatel import dom
>>> fact0 = dom.Fact(0, attr0=1, attr1=None)
>>> fact1 = dom.Fact(1, attr0=1)

>>> fact0 == fact1

>>> fact0 is fact1

>>> set([fact0, fact1])
{<Fact (of Haplotype '0') at 0x22e75d0>,
 <Fact (of Haplotype '1') at 0x22e78d0>}