Add dunder methods to the Python Record class

[apcamargo]

This PR introduces several dunder methods to the Python Record class:

• __new__: Constructor that allows the direct creation of Record objects:

>>> fasta_record = needletail.Record("SRR1749083.HWI-ST1309F", "NGACTCGTC")
>>> fastq_record = needletail.Record("SRR1749083.HWI-ST1309F", "NGACTCGTC", "#<<BBF/FF")

• __hash__: Returns an integer hash based on the record's ID, sequence, and quality (if available). This overrides the default __hash__, which generates different hashes for identical objects.
• __eq__: Compares two Record objects by checking if their IDs, sequences, and qualities (if available) are identical. While we could check for equality based on hashes, this would involve additional computation.
• __len__: Returns the length of the sequence, similar to BioPython's behavior.
• __str__: Returns a string formatted in FASTA/FASTQ style to facilitate writing FASTX files. Currently, sequences are wrapped at 60 characters for FASTA records, though the wrapping can be adjusted.
• __repr__: Provides a simple string representation that includes the record ID, a sequence snippet, and the quality string (when available):

>>> needletail.Record("SRR1749083.HWI-ST1309F", "NGACTCGTC")
# Record(id=SRR1749083.HWI-ST1309F, sequence=NGACTCGTC, quality=None)

Additionally, is_fasta and is_fastq have been converted to properties.

Test coverage for these methods has not been added yet, but I will implement it if this PR is approved.

[audy]

@apcamargo thank you very much! I left some comments. Otherwise, these changes look like great additions to the library and we'd be happy to merge them in.

[apcamargo]

Thanks for the review, @audy! I just pushed commits that address all your comments.

I prefer wrapping since that's how other libraries/tools format FASTAs, and I think users expect it. That said, I’m not too attached to it :)

[audy]

@apcamargo thanks for making those changes. Let me know if you're good to merge.

[apcamargo]

@audy I’ve added docstrings to all classes, methods, and functions. The only potential change I’d consider is adding a default value to the iupac parameter in both normalize_seq and normalize.

[apcamargo]

@audy I also updated parse_fastx_file to make it able to take pathlib.Path objects, in addition to str.

[audy]

@apcamargo Awesome! Do you mind adding some tests?

The only potential change I’d consider is adding a default value to the iupac parameter in both normalize_seq and normalize.

I support this change but I'm not sure if it should default to True or False. Thoughts?

[apcamargo]

Apologies, @audy! I had forgotten about the tests.

I've now added tests for all the new functions and methods, and set the default value of iupac to False.