feat: Add parameter validation for `OffTargetDetector.init` #103

ameynert · 2025-01-07T17:49:42Z

max_amplicon_size > 0
max_primer_hits >= 0
max_primer_pair_hits >= 0
min_primer_pair_hits >= 0
three_prime_region_length > 0
0 <= max_mismatches_in_three_prime_region <= three_prime_region_length
max_mismatches >= 0
max_gap_opens >= 0
max_gap_extends == -1 or max_gap_extends >= 0

codecov · 2025-01-07T17:54:21Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.81%. Comparing base (baf2e65) to head (ac16e3c).
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #103      +/-   ##
==========================================
+ Coverage   96.77%   96.81%   +0.04%     
==========================================
  Files          26       26              
  Lines        1766     1789      +23     
  Branches      205      215      +10     
==========================================
+ Hits         1709     1732      +23     
  Misses         31       31              
  Partials       26       26

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tfenne

Thanks for doing this @ameynert. Looks great but would like us to settle on a higher min for 3' region length before merging please. If @nh13 doesn't respond, I think we could set that to 10 for now.

tfenne · 2025-01-10T22:13:07Z

prymer/offtarget/offtarget_detector.py

+        if three_prime_region_length < 1:
+            errors.append(
+                "'three_prime_region_length' must be greater than 0. "
+                f"Saw {three_prime_region_length}"
+            )


Given that we use this to drive the "seed region" for bwa I think we should probably enforce a higher miniumum. @nh13 do you have a thought on what's reasonable? E.g. 8, 10, 12 or somewhere around there?

I agree that since this value is use for the seed length, we should (1) add that explanation to the parameter or class docs, and (2) have a minimum of 8.

…plicon_size and three_prime_region_length

…gion error message

ameynert · 2025-01-10T23:07:49Z

I've added checks for max_gap_opens and max_gap_extends as well. Will wait on @nh13 to agree on a min for 3' region length before merging.

coderabbitai · 2025-01-10T23:09:19Z

Walkthrough

The changes enhance parameter validation in the OffTargetDetector class located in offtarget_detector.py. A new constant, MINIMUM_THREE_PRIME_REGION_LENGTH, is introduced, and the constructor now enforces explicit constraints on several parameters, including max_amplicon_size and three_prime_region_length. Violations of these constraints result in ValueError exceptions with specific messages. Additionally, a new test function, test_init, is added to test_offtarget.py to validate these constraints during initialization, ensuring that improper configurations are detected and reported effectively.

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📒 Files selected for processing (2)

prymer/offtarget/offtarget_detector.py (3 hunks)
tests/offtarget/test_offtarget.py (2 hunks)

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GitHub Check: Tests (3.12)
GitHub Check: Tests (3.11)

🔇 Additional comments (4)

prymer/offtarget/offtarget_detector.py (3)

107-109: Good addition of the minimum seed length constant.

Defining MINIMUM_THREE_PRIME_REGION_LENGTH ensures a consistent minimum for the seed length.

195-196: Clear documentation of three_prime_region_length.

Specifying that three_prime_region_length is used as the seed length for bwa aln enhances clarity.

247-293: Effective parameter validation implemented.

The constructor correctly validates parameters and raises ValueError with informative messages when constraints are violated.

tests/offtarget/test_offtarget.py (1)

355-401: Comprehensive tests for constructor validation.

The test_init function thoroughly checks parameter constraints, ensuring ValueError is raised appropriately for invalid inputs.

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tfenne · 2025-01-13T22:39:45Z

@ameynert as things have gotten a bit complicated, why don't we merge this with three_prime_region_length > 0 and we can circle back and increase it as/when we see fit?

ameynert marked this pull request as ready for review January 7, 2025 18:03

ameynert requested review from nh13 and tfenne as code owners January 7, 2025 18:03

ameynert self-assigned this Jan 7, 2025

tfenne approved these changes Jan 10, 2025

View reviewed changes

Base automatically changed from am_primer_pair_hit_building to main January 10, 2025 22:50

ameynert added 6 commits January 10, 2025 14:54

feat: add validation to initiation of OffTargetDetector

a06dc5b

feat: simplified error messages to strictly greater than 0 for max_am…

924dd6d

…plicon_size and three_prime_region_length

feat: added unit tests for OffTargetDetector.__init__ validation

52dddf1

feat: description of ValueErrors matches error messages

b5c2354

feat: added parameter name range for max_mixmatches_in_three_prime_re…

cdca0bf

…gion error message

feat: added post init checks for max_gap_opens and max_gap_extends

c9075ac

ameynert force-pushed the am_overlap_detector_post_init_validation branch from 1a61cb0 to c9075ac Compare January 10, 2025 23:06

coderabbitai bot approved these changes Jan 10, 2025

View reviewed changes

feat: set minimum 3 prime region length to 8, added context to docstring

ac16e3c

ameynert merged commit a193734 into main Jan 13, 2025
7 checks passed

ameynert deleted the am_overlap_detector_post_init_validation branch January 13, 2025 23:26

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feat: Add parameter validation for `OffTargetDetector.init` #103

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feat: Add parameter validation for OffTargetDetector.__init__ #103

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feat: Add parameter validation for `OffTargetDetector.init` #103

feat: Add parameter validation for `OffTargetDetector.init` #103

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