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Add the phred_quality_score method to the Python Record class #98

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Merged
merged 6 commits into from
Apr 7, 2025
Merged

Add the phred_quality_score method to the Python Record class #98

merged 6 commits into from
Apr 7, 2025
+65 −16

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apcamargo
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@apcamargo apcamargo commented Feb 15, 2025 •
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This PR introduces the decode_phred function that takes in a string representing Phred-encoded quality scores and returns a tuple of integers representing the quality scores themselves. The function uses Phred+33 by default and allows the user to use Phred+64 via the base_64 parameter.

>>> from needletail import decode_phred
>>> decode_phred("#</</BBFFFBF<")
(2, 27, 14, 27, 14, 33, 33, 37, 37, 37, 33, 37, 27)

audy
audy requested changes Feb 15, 2025
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@apcamargo I think it's probably worth adding this to SequenceRecord in the underlying Rust implementation.

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Thanks, @audy. I don't have much familiarity with the Rust library. Could you provide any pointers of where this should go? Maybe a method for SequenceRecord in record.rs?

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audy commented Mar 7, 2025

Thanks, @audy. I don't have much familiarity with the Rust library. Could you provide any pointers of where this should go? Maybe a method for SequenceRecord in record.rs?

I think the best place is probably parser/record.rs. parser/fastq.rs has methods for returning data straight from the file buffer. But since this requires some transformation of that data, I think parser/record.rs makes the most sense.

@apcamargo apcamargo mentioned this pull request Apr 1, 2025
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@audy I updated this PR to use the functions from the Rust library. I also moved the function out of the Record class to keep it consistent with reverse_complement. Tests were updated accordingly.

normalize is still the odd one out since it also exists as a method that modifies the object. Maybe we can think about making things more consistent in a future breaking update?

audy
audy approved these changes Apr 7, 2025
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Looks good to me!

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audy commented Apr 7, 2025 •
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normalize is still the odd one out since it also exists as a method that modifies the object. Maybe we can think about making things more consistent in a future breaking update?

I think I would prefer a method that returns a new SequenceRecord with a normalized sequence (same in the underlying Rust implementation) rather than modifying the record in place. What do you think @apcamargo?

@audy audy merged commit d1fdc35 into onecodex:master Apr 7, 2025
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Agreed! Let me know how you prefer to do this, since it would break the API

@apcamargo apcamargo deleted the python-phred-quality-score branch April 18, 2025 22:45
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