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hyanwong / giglib

MIT License
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Tandem duplications #100

Open hyanwong opened 8 months ago

hyanwong commented 8 months ago

WIP. You can test by running the following code:

from collections import Counter

from tests.test_gigutil import TestDTWF_one_break_no_rec_inversions_slow

test = TestDTWF_one_break_no_rec_inversions_slow()
test.progress_monitor = True
test.default_gens = 40  # increase number of gens for more consistent profiling
print(f"Duplication: {test.duplication} (size = {test.duplication.span} bp)")
test.test_tandem_duplication()
gig = test.gig.sample_resolve()
sample_lengths = [
    (gig.tables.iedges.child_right[gig.tables.iedges.child == s]).max()
    for s in gig.samples
]
c = Counter(sample_lengths)
print(c)
print("num edges", len(test.gig.iedges), ". Simplified to", len(gig.iedges))

For me, this takes about 10 mins, and results in a list of genome sizes that have lengths that differ by multiples of 450bp (the duplication size)

Duplication: Interval(left=50, right=500) (size = 450 bp)
Simulating: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 158.86gen/s]
Simulating more: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████| 39/39 [10:36<00:00, 16.32s/gen]
Counter({531: 96, 981: 64, 1431: 22, 1881: 11, 2331: 4, 2781: 2, 3231: 1})
num edges 15591 . Simplified to 8860

Summary by CodeRabbit

coderabbitai[bot] commented 8 months ago

Walkthrough

This update enhances a genetic simulation utility, focusing on progress monitoring during simulations and supporting structural variations (SVs) like tandem duplications. It improves user experience by integrating tqdm for progress tracking and refines the simulation's flexibility and accuracy by adjusting parameters related to validation and SV handling.

Changes

Files Change Summary
tests/gigutil.py Added tqdm.auto import, replaced use_validation with skip_validate, added progress_monitor.
tests/test_gigutil.py Added constants and attributes for duplication and validation, updated method calls for progress monitoring and SV handling.
GeneticInheritanceGraphLibrary/tables.py Updated field type definitions for non-integer fields to enhance space efficiency.
tests/test_tables.py Added a test method for adding edges with negative chromosome numbers, included assertions for negative values.
requirements.txt Added tqdm package.

Related issues

Poem

In fields of code where logic hops,
🐇 A rabbit toils by lines and ops.
With progress bars that smoothly slide,
And duplications far and wide.
Through loops and functions, swift it leaps,
In binary burrows, deep it peeps.
"To simulate," it softly sings,
"Is to give data wings." 🚀

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