9318012713

Committed 31 May 2024 12:17PM UTC coverage: 56.276% (+0.5%) from 55.813%

Build # 9318012713

Build Type

push

github

Committed by

holmrenser

Commit Message

bugfix: gtf file writing

Run Details

315 of 580 branches covered (54.31%)

Branch coverage included in aggregate %.

27 of 41 new or added lines in 4 files covered. (65.85%)

4 existing lines in 2 files now uncovered.

631 of 1101 relevant lines covered (57.31%)

5.16 hits per line

Source File
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15.31

/picea/ontology.py

import warnings
from collections import defaultdict
from itertools import groupby
from typing import List

from .dag import DAGElement, DirectedAcyclicGraph


class OntologyTerm(DAGElement):
    _predefined_ontology_elements = ("name", "def")

    def __init__(self, ID, parents, container, **kwargs):
        super().__init__(ID=ID, parents=parents, container=container)

        for attr in self._predefined_ontology_elements:
            self[attr] = kwargs.get(attr, None)

        for key, value in kwargs.items():
            self[key] = value


class Ontology(DirectedAcyclicGraph):
    def __init__(self):
        super().__init__()
        self._header: List[str] = []

    def __getitem__(self, ID) -> OntologyTerm:
        term = self._elements[ID]
        if not term._children and not term._parents and term.__dict__.get("alt_id"):
            alt_id = term.__dict__.get("alt_id")[0]
            term = self._elements[alt_id]
            warnings.warn(f"Accessed GO term by alt ID {ID}, " f"returning main GO term with ID {alt_id}")
        return term

    @classmethod
    def from_obo(cls, filename: str = None, string: str = None, skip_obsolete=True) -> "Ontology":
        assert filename or string
        assert not (filename and string)
        ontology = cls()
        if filename:
            with open(filename) as filehandle:
                string = filehandle.read()

        obo_iter = (el for _, el in groupby(string.strip().split("\n"), lambda line: line[:1] == "["))

        ontology._header = list(next(obo_iter))

        for element in obo_iter:
            element = next(element)
            if element != "[Term]":
                continue
            attributes = defaultdict(list)
            for attribute in next(obo_iter):
                if not attribute:
                    continue
                attr_key, attr_value = attribute.split(":", 1)
                attributes[attr_key].append(attr_value.strip())
            if skip_obsolete and attributes.get("is_obsolete"):
                continue

            ID = attributes.pop("id")[0].strip()
            parents = [p.split("!")[0].strip() for p in attributes.get("is_a", "")]

            for relationship in attributes.get("relationship", []):
                relation_type, go_id = relationship.split("!")[0].strip().split(" ")
                if relation_type == "part_of":
                    parents.append(go_id)

            alt_ids = {*attributes.pop("alt_id", []), ID}
            for alt_id in alt_ids:
                ontology[alt_id] = OntologyTerm(
                    ID=alt_id,
                    parents=parents,
                    container=ontology,
                    alt_id=[id for id in alt_ids if id != alt_id],
                    **attributes,
                )

        for ontology_term in ontology:
            for parent_id in ontology_term._parents:
                parent_term = ontology[parent_id]
                parent_term._children.append(ontology_term.ID)

        return ontology

1	import warnings	9✔
2	from collections import defaultdict	9✔
3	from itertools import groupby	9✔
4	from typing import List	9✔
5
6	from .dag import DAGElement, DirectedAcyclicGraph	9✔
7
8
9	class OntologyTerm(DAGElement):	9✔
10	_predefined_ontology_elements = ("name", "def")	9✔
11
12	def __init__(self, ID, parents, container, **kwargs):	9✔
13	super().__init__(ID=ID, parents=parents, container=container)	×
14
15	for attr in self._predefined_ontology_elements:	×
16	self[attr] = kwargs.get(attr, None)	×
17
18	for key, value in kwargs.items():	×
19	self[key] = value	×
20
21
22	class Ontology(DirectedAcyclicGraph):	9✔
23	def __init__(self):	9✔
24	super().__init__()	×
25	self._header: List[str] = []	×
26
27	def __getitem__(self, ID) -> OntologyTerm:	9✔
28	term = self._elements[ID]	×
29	if not term._children and not term._parents and term.__dict__.get("alt_id"):	×
30	alt_id = term.__dict__.get("alt_id")[0]	×
31	term = self._elements[alt_id]	×
NEW 32	warnings.warn(f"Accessed GO term by alt ID {ID}, " f"returning main GO term with ID {alt_id}")	×
UNCOV 33	return term	×
34
35	@classmethod	9✔
36	def from_obo(cls, filename: str = None, string: str = None, skip_obsolete=True) -> "Ontology":	9✔
UNCOV 37	assert filename or string	×
38	assert not (filename and string)	×
39	ontology = cls()	×
40	if filename:	×
41	with open(filename) as filehandle:	×
42	string = filehandle.read()	×
43
NEW 44	obo_iter = (el for _, el in groupby(string.strip().split("\n"), lambda line: line[:1] == "["))	×
45
46	ontology._header = list(next(obo_iter))	×
47
48	for element in obo_iter:	×
49	element = next(element)	×
50	if element != "[Term]":	×
51	continue	×
52	attributes = defaultdict(list)	×
53	for attribute in next(obo_iter):	×
54	if not attribute:	×
55	continue	×
56	attr_key, attr_value = attribute.split(":", 1)	×
57	attributes[attr_key].append(attr_value.strip())	×
58	if skip_obsolete and attributes.get("is_obsolete"):	×
59	continue	×
60
61	ID = attributes.pop("id")[0].strip()	×
62	parents = [p.split("!")[0].strip() for p in attributes.get("is_a", "")]	×
63
64	for relationship in attributes.get("relationship", []):	×
65	relation_type, go_id = relationship.split("!")[0].strip().split(" ")	×
66	if relation_type == "part_of":	×
67	parents.append(go_id)	×
68
69	alt_ids = {*attributes.pop("alt_id", []), ID}	×
70	for alt_id in alt_ids:	×
71	ontology[alt_id] = OntologyTerm(	×
72	ID=alt_id,
73	parents=parents,
74	container=ontology,
75	alt_id=[id for id in alt_ids if id != alt_id],
76	**attributes,
77	)
78
79	for ontology_term in ontology:	×
80	for parent_id in ontology_term._parents:	×
81	parent_term = ontology[parent_id]	×
82	parent_term._children.append(ontology_term.ID)	×
83
84	return ontology	×

holmrenser / picea / 9318012713

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