add example of #[pyclass] usage

[davidhewitt]

Hello! Just pushing this example following our chat right now.

Feel free to ping me to ask further, hope this proves useful to play with 🚀

[LCrossman]

Hi, thanks this is greatly helpful

[LCrossman]

@davidhewitt following up....

see changes in: branch

• wrote pytests, previously only had a rust test that functions were added to the pymodule
• converted the Faa pyclass we talked about to a SequenceCollection as below for a more generic use to handle both Faa (protein sequence) and Ffn (gene sequence)
• created the following pyclasses and return types:

PyRecord:

• has pymethods write_faa, write_ffn, and write_fna which write directly to file
• wraps InternalRecord (either gbk or embl), has .sequences() and .features() pymethods returning multiple features and sequences gene data as a HashMap<String, Py>

SequenceCollection - is a HashMap<String, Py>, created by PyRecord .sequences() or directly conversion functions gbk_to_faa etc. , returns as a PyResult

FeatureCollection - is a HashMap<String, Py>, created by PyRecord pymethod .features()

RecordCollection - HashMap<String, Py>, top-level return of parse_gbk/parse_embl, returns as a PyResult

PyFeatureInfo - contains per single gene info: key: locus_tag, gene, product, start, stop, strand, codon_start, extras (extras is a store for optional tags that can crop up like old_locus_tag etc)

PySequenceInfo - contains per single gene info: key: locus_tag, sequence_faa (protein), sequence_ffn (gene sequence), extras

LocusTagIterator - key iterator returned by iter on any collection.

Future - moving away from a separate gbk, embl (stored in InternalRecord) towards a more generic record on the Rust side so built with that in mind for ease of later change.

I am getting: (mac osx benchmarks)
microBioRust Rust-only benchmarking file conversion: 79.9 ms
microbiorust-py using write_faa directly: 86.9 ms
microbiorust-py using .sequences() returning PyResult<String, Py>: 90.4 ms

Big improvement on python integration!

• planning to integrate at the end of the week - please comment if you have time or comments

[LCrossman]

Closing this with thanks, as integrated into microbiorust-py with pyclasses and pymethods