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hyanwong / giglib

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Add the graph object #46

Closed hyanwong closed 10 months ago

hyanwong commented 10 months ago

To represent a immutable, valid GIG. This also includes a method to "sample resolve" a GIG, although it's not extensively tested yet.

@duncanMR - after writing the code, I think that it's easier to have child_left < child_right for inversions (rather than the same for parents), because in my sample_resolve code, I check the left and right in the child against the existing intervals as we go up the graph. See what you think?

There's a lot of extra functionality in this PR, sorry, but I think it's useful. I've tried to stick to the tskit style as much as possible, apart from the following:

gig.edges  # can iterate over, like ts.edges() but without the braces
gig.edges[0]  # same as ts.edge(0)
gig.nodes  # like ts.nodes()
gig.node[0]  # like ts.node(0)
gig.sequence_length(u)  # has to be per node: find a max sequence length for node u, using the edges

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Commits Files that changed from the base of the PR and between baece7f2be2962a540033806ad21c531691555c2 and 1f82ee77e2bd02e82757fea5673bc9010aefd8f6.

Walkthrough

The GeneticInheritanceGraph library has undergone a significant update, introducing new imports, classes, and methods across various modules. These changes enhance the library's ability to represent and manipulate genetic inheritance graphs. Additionally, the update includes a naming convention shift from gig to gigl, reflected across import statements and test cases, indicating a move towards a more efficient and feature-rich library.

Changes

File Path Summary of Changes
.../GeneticInheritanceGraph/__init__.py Added imports for from_tree_sequence and Graph from the graph module.
.../GeneticInheritanceGraph/graph.py Introduced Graph class, from_tree_sequence function, and data classes IEdge and Node.
.../GeneticInheritanceGraph/tables.py Enhanced table row classes with @dataclass, added new methods to BaseTable and Tables.
tests/conftest.py
tests/gigutil.py
tests/test_graph.py
tests/test_tables.py
tests/test_util.py		 Renamed module import to gigl, updated fixtures, and revised test cases to reflect the new naming convention.

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Through graphs and nodes, it never stops.
With changes wrought, the tests align,
Inheritance graphs, now more divine.
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hyanwong commented 10 months ago

I'm please that the sample_resolve algorithm is so simple (this is the core of the simplify method), although it needs a lot more testing. I did have to use an interval library though. I does correctly sample resolve the sv gig (https://github.com/hyanwong/GeneticInheritanceGraph/issues/2#issuecomment-1858383674)

codecov-commenter commented 10 months ago

Codecov Report

Attention: 9 lines in your changes are missing coverage. Please review.

Comparison is base (cceee86) 89.30% compared to head (331bff1) 92.24%. Report is 1 commits behind head on main.

Files Patch % Lines
GeneticInheritanceGraph/graph.py 95.03% 3 Missing and 5 partials :warning:
GeneticInheritanceGraph/tables.py 97.72% 1 Missing :warning:

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #46 +/- ## ========================================== + Coverage 89.30% 92.24% +2.94% ========================================== Files 4 5 +1 Lines 187 387 +200 Branches 35 81 +46 ========================================== + Hits 167 357 +190 - Misses 5 11 +6 - Partials 15 19 +4 ```

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duncanMR commented 10 months ago

LGTM! I haven't analysed sample_resolve in-depth but I'll get to that in future

hyanwong commented 10 months ago

LGTM! I haven't analysed sample_resolve in-depth but I'll get to that in future

Thanks. That routine almost certainly needs more testing, but once you've had a look over it, I guess I should merge, and we can add tests later?

hyanwong commented 10 months ago

Note that the sample_resolve function (including the comment) is largely from https://github.com/tskit-dev/tskit/discussions/2869#discussioncomment-7553044

duncanMR commented 10 months ago

I cooked up a quick example with a deletion and a subtree without samples, and it behaved exactly as expected:

image

import GeneticInheritanceGraph as gigl
import tests.gigutil as gigutil

    # p | c | c_left | c_right | p_left | p_right
interval_data = [
    (10, 8, 0, 3, 0, 3),
    (10, 9, 0, 5, 5, 0),
    (8, 4, 0, 3, 0, 3),
    (8, 4, 3, 6, 0, 3),
    (9, 6, 0, 5, 0, 5),
    (9, 7, 0, 5, 0, 5),
    (4, 0, 0, 6, 0, 6),
    (4, 1, 0, 6, 0, 6),
    (5, 2, 0, 3, 0, 3),
    (5, 3, 0, 3, 0, 3)
]
# time | flags
node_data = [
    (0, 1),
    (0, 1),
    (0, 1),
    (0, 1),
    (1, 0),
    (1, 0),
    (1, 0),
    (1, 0),
    (2, 0),
    (2, 0),
    (4, 0)
]

tables = gigl.Tables()
tables.intervals = gigutil.make_iedges_table(interval_data, tables)
tables.nodes = gigutil.make_nodes_table(node_data, tables)
tables.sort()
gig = gigl.Graph(tables)
resolved_gig = gig.sample_resolve()
print(gig.tables)
print(resolved_gig.tables)

I agree that we should merge it. It seems to work fine for simple examples; once we have a forward simulator, we'll be able to write more rigorous tests.

hyanwong commented 10 months ago

Great, thanks a lot for testing. I'll merge this now.