feat: overloaded 'SeqDict.from_sam()' method to support SAM files (#176) #183
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TimD1
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Sep 4, 2024
TimD1
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- in addition to pysam SAM headers and SAM header dicts, SeqDicts can now be initialized from SAM file paths and pysam SAM files
- added basic tests for this new functionality
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #183 +/- ##
==========================================
- Coverage 91.06% 90.78% -0.28%
==========================================
Files 18 18
Lines 2283 2301 +18
Branches 337 339 +2
==========================================
+ Hits 2079 2089 +10
- Misses 133 142 +9
+ Partials 71 70 -1 ☔ View full report in Codecov by Sentry. |
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- in addition to pysam SAM headers and SAM header dicts, SeqDicts can now be initialized from SAM file paths and pysam SAM files - added basic tests for this new functionality
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WalkthroughThe pull request introduces changes to the Additionally, the 📜 Recent review detailsConfiguration used: CodeRabbit UI 📒 Files selected for processing (1)
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Actionable comments posted: 1
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fgpyo/fasta/sequence_dictionary.py(4 hunks)pyproject.toml(1 hunks)tests/fgpyo/fasta/test_sequence_dictionary.py(3 hunks)
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- GitHub Check: testing (3.10)
- GitHub Check: testing (3.9)
🔇 Additional comments (3)
fgpyo/fasta/sequence_dictionary.py (1)
481-499:from_sammethod implementation effectively handles multiple input types.The use of an
if-elif-elsechain improves readability and accommodates various data inputs as specified.tests/fgpyo/fasta/test_sequence_dictionary.py (1)
335-338: Test cases validate newfrom_samfunctionality.The added tests ensure that the method correctly processes
Pathandpysam.AlignmentFileinputs.pyproject.toml (1)
92-96: Excluding@overloadannotations from coverage improves report accuracy.Adjusting the coverage configuration aligns with best practices for handling type stubs.
| except Exception as e: | ||
| raise ValueError(f"Could not parse sequence information from data: {data}") from e |
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🛠️ Refactor suggestion
Avoid including raw data in exception messages.
Including the entire data object in the error message may lead to verbose logs or expose sensitive information. Consider providing a more general error message.
Apply this diff to adjust the error message:
-except Exception as e:
- raise ValueError(f"Could not parse sequence information from data: {data}") from e
+except Exception as e:
+ raise ValueError("Could not parse sequence information from provided data.") from e📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| except Exception as e: | |
| raise ValueError(f"Could not parse sequence information from data: {data}") from e | |
| except Exception as e: | |
| raise ValueError("Could not parse sequence information from provided data.") from e |
| A `SequenceDictionary` mapping refrence names to their metadata. | ||
| """ | ||
| seq_dict: SequenceDictionary | ||
| if isinstance(data, pysam.AlignmentHeader): |
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this is begging for a structural pattern (class pattern) but I think our min python version is 3.9 :/
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| return seq_dict | ||
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| # TODO: mypy doesn't like these |
| @@ -88,3 +88,9 @@ warn_unused_configs = true | |||
| warn_unused_ignores = true | |||
| enable_error_code = "ignore-without-code" | |||
| exclude = ["site/", "docs/"] | |||
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| [tool.coverage.report] | |||
| @@ -333,10 +332,15 @@ def test_sequence_dictionary_to_and_from_sam() -> None: | |||
| header = pysam.AlignmentHeader.from_dict( | |||
| header_dict={"HD": {"VN": "1.5"}, "SQ": mapping, "RG": [{"ID": "foo"}]} | |||
| ) | |||
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| samfile: Path = builder.SamBuilder(sd=mapping).to_path() | |||
| alignment: pysam.AlignmentFile = reader(samfile) | |||
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use with a with statement so it automatically closes.
