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LCrossmanLCrossman
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adding seqmetrics functions to microbiorust-py
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‎microbiorust-py/Cargo.toml‎

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@@ -27,3 +27,5 @@ extension-module = ["pyo3/extension-module"]
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[dependencies]
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microBioRust = "0.1.2"
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microBioRust-seqmetrics = "0.1.2"
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‎microbiorust-py/K12_ribo.gbk‎

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LOCUS NC_000913 913 bp DNA linear CON 01-Sep-2025
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DEFINITION Escherichia coli
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ACCESSION NC_000913
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KEYWORDS .
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SOURCE Escherichia coli str. K-12 substr. MG1655
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ORGANISM Escherichia coli str. K-12 substr. MG1655
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Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
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Enterobacterales; Enterobacteriaceae; Escherichia.
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FEATURES Location/Qualifiers
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source <1..>913
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/id="source_1"
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/organism="Escherichia coli str. K-12 substr. MG1655"
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/mol_type="genomic DNA"
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/strain="K-12"
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/sub_strain="MG1655"
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/db_xref="taxon:511145"
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source complement(1..913)
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gene complement(10..363)
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/gene="rplR"
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/locus_tag="b3304"
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/gene_synonym="ECK3291"
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/db_xref="ASAP:ABE-0010825"
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/db_xref="ECOCYC:EG10879"
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/db_xref="GeneID:947804"
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CDS complement(10..363)
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/gene="rplR"
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/locus_tag="b3304"
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/gene_synonym="ECK3291"
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/codon_start=1
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/transl_table=11
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/product="50S ribosomal subunit protein L18"
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/protein_id="NP_417763.1"
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/db_xref="UniProtKB/Swiss-Prot:P0C018"
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/db_xref="ASAP:ABE-0010825"
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/db_xref="ECOCYC:EG10879"
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/db_xref="GeneID:947804"
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/translation="MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNG
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SEVLVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGR
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VQALADAAREAGLQF"
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gene complement(373..906)
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/gene="rplF"
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/locus_tag="b3305"
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/gene_synonym="ECK3292"
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/db_xref="ASAP:ABE-0010827"
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/db_xref="ECOCYC:EG10869"
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/db_xref="GeneID:947803"
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CDS complement(373..906)
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/gene="rplF"
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/locus_tag="b3305"
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/gene_synonym="ECK3292"
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/codon_start=1
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/transl_table=11
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/product="50S ribosomal subunit protein L6"
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/protein_id="NP_417764.1"
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/db_xref="UniProtKB/Swiss-Prot:P0AG55"
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/db_xref="ASAP:ABE-0010827"
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/db_xref="ECOCYC:EG10869"
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/db_xref="GeneID:947803"
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/translation="MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVK
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HADNTLTFGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNV
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INLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGK
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GVRYADEVVRTKEAKKK"
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BASE COUNT 214 a 256 c 223 g 220 t
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ORIGIN
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1 acctctacct tagaactgaa ggccagcttc acgggcagca tctgccagtg cctggacacg
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61 accatgatat tggaacccgg aacggtcaaa ggatacatct ttgatgcctt tttccagagc
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121 gcgttcagcg acagctttac ccacagctgc agccgcgtct ttgttaccgg tgtacttcag
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181 ttgttcagcg atagcttttt ctacagtaga agcagctacc agaacttcag aaccgttcgg
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241 tgcaattacc tgtgcgtaaa tgtgacgcgg ggtacgatgt accaccaggc gagttgcgcc
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301 cagctcctgg agcttgcggc gtgcgcgggt cgcacgacgg atacgagcag atttcttatc
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361 catagtgtta ccttacttct tcttagcctc tttggtacgc acgacttcgt cggcgtaacg
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421 aacacccttg cctttataag gctcaggacg acggtaggcg cgcagatccg ctgcaacctg
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481 gccgatcacc tgcttatcag cgcctttcag cacgatttca gtctgagtcg gacattcagc
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541 agtgataccc gcaggcagct gatggtcaac aggatgagag aaacccagag acaggttaat
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601 cacattgcct ttaaccgctg cacggtaacc tacaccaacc agctgcagct tcttagtgaa
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661 gccttcggta acaccgataa ccattgagtt cagcagggca cgcgcggtac cagcctgtgc
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721 ccaaccgtct gcgtaaccat cacgcggacc gaaggtcagg gtattatctg catgtttaac
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781 ttcaacagca tcgttgagag tacgagtcag ctcgccgttt ttacctttga tcgtaataac
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841 ctgaccgttg atttttacgt caacgccggc aggaacaacg accggtgctt tagcaacacg
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901 agacattttt tcc
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//

‎microbiorust-py/src/lib.rs‎

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//!
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//! Once developed, the PyModule can be loaded into Python and used:
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//!
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//! import microbiorust
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//! from microbiorust import gbk_to_faa
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//! result = gbk_to_faa("test_input.gbk")
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//! for r in result:
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//! print(r)
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//! gbk_to_gff("test_input.gbk")
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//!
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//! Other pyfunctions that can be run include gbk_to_faa, embl_to_faa, gbk_to_gff and embl_to_gff
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//! Other pyfunctions that can be run include gbk_to_faa, embl_to_faa, gbk_to_gff, embl_to_gff, amino_counts, amino_percentage, hydrophobicity
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//!
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//! from microbiorust import amino_percentage
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//! result = amino_percentage("MSNTQKKNVPELRFPGFEGEWEEKKLGDLTTKIGSGKTPKGGSENYTNKGIPFLRSQNIRNGKLNLNDLVYISKDIDDEMKNSRTY")
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//! print(result)
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use pyo3::{
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prelude::*,
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types::PyModule,
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};
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use microBioRust::genbank;
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use std::collections::HashMap;
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use std::{
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collections::BTreeMap,
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io::{self, Write},
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use microBioRust::gbk::{Record, Reader, RangeValue, gff_write};
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use microBioRust::embl;
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use microBioRust::embl::gff_write as embl_gff_write;
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use microBioRust_seqmetrics::metrics::hydrophobicity as rust_hydrophobicity;
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use microBioRust_seqmetrics::metrics::amino_counts as rust_amino_counts;
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use microBioRust_seqmetrics::metrics::amino_percentage as rust_amino_percentage;
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#[pyfunction]
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fn gbk_to_faa(filename: &str) -> PyResult<Vec<String>> {
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return Ok(());
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}
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#[allow(unused_imports)]
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#[allow(unused_variables)]
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#[pyfunction]
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fn hydrophobicity(seq: &str, window_size: usize) -> Vec<f64> {
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rust_hydrophobicity(seq, window_size)
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}
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#[allow(unused_imports)]
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#[allow(unused_variables)]
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#[pyfunction]
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fn amino_percentage(seq: &str) -> HashMap<char,f64> {
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rust_amino_percentage(seq)
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}
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#[allow(unused_imports)]
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#[allow(unused_variables)]
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#[pyfunction]
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fn amino_counts(seq: &str) -> HashMap<char, u64> {
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rust_amino_counts(seq)
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}
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#[pymodule]
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fn microbiorust(m: &Bound<'_, PyModule>) -> PyResult<()> {
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fn microbiorust(py: Python, m: &Bound<'_, PyModule>) -> PyResult<()> {
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m.add_function(wrap_pyfunction!(gbk_to_faa, m)?)?;
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m.add_function(wrap_pyfunction!(embl_to_faa, m)?)?;
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m.add_function(wrap_pyfunction!(gbk_to_gff, m)?)?;
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m.add_function(wrap_pyfunction!(embl_to_gff, m)?)?;
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m.add_function(wrap_pyfunction!(hydrophobicity, m)?)?;
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m.add_function(wrap_pyfunction!(amino_counts, m)?)?;
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m.add_function(wrap_pyfunction!(amino_percentage, m)?)?;
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Ok(())
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}
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#[cfg(test)]
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mod tests {
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use crate::microbiorust;
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fn test_functions_are_registered() {
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Python::with_gil(|py| {
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let m = PyModule::new(py, "microbiorust").unwrap();
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microbiorust(&m).unwrap();
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for func in &["gbk_to_faa", "embl_to_faa", "gbk_to_gff", "embl_to_gff"] {
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microbiorust(py, &m).unwrap();
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for func in &["gbk_to_faa", "embl_to_faa", "gbk_to_gff", "embl_to_gff", "hydrophobicity", "amino_counts", "amino_percentage"] {
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assert!(m.getattr(func).is_ok(), "Function {} not found", func);
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}
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});
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}
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}

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