version 0.1.4 final

.gitignore

@@ -1,7 +1,17 @@
 # Generated by Cargo
 # will have compiled files and executables
-debug/
 target/
+dist/
+*.egg-info/
+__pycache__/
+*.pyc
+debug/
+
+*.so
+*.abi3.so
+*.dylib
+*.pyd
+
 expand.rs
 # Remove Cargo.lock from gitignore if creating an executable, leave it for libraries
 # More information here https://doc.rust-lang.org/cargo/guide/cargo-toml-vs-cargo-lock.html
@@ -25,3 +35,4 @@ env/
 venv/
 site/
 static/
+*.gff

microBioRust/Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "microBioRust"
-version = "0.1.3"
-edition = "2021"
+version = "0.1.4"
+edition = "2024"
 license = "MIT"
 keywords = ["bioinformatics", "micro", "bio", "genomics", "sequence-analysis"]
 description = "Microbiology friendly bioinformatics Rust functions"
@@ -14,7 +14,7 @@ categories = [
 ]
 readme = "README.md"
 authors = ["Lisa Crossman and microBioRust community"]
-exclude = [".git", ".gitignore", ".dribble.example.embl", "tests/data/"]
+exclude = [".git", ".gitignore", ".dribble.example.embl", "tests/", "src/bin","config.toml","K12_ribo.gbk","Rhiz3841.gbk.gb","Rhiz3841.gbk.gb_out.faa","rust_via_python_countgbk2faa.py","rust_via_python_gbk2faa.py","asv.conf.json","benchmarks/"]
 repository = "https://github.com/microBioRust/microBioRust"
 documentation = "https://microbiorust.github.io/docs/"
 
@@ -27,7 +27,11 @@ path = "src/lib.rs"
 
 [[example]]
 name = "blast-example"
-path = "examples/src/blast_parse.rs"
+path = "examples/blast_parse.rs"
+
+[[example]]
+name = "convert-to-faa"
+path = "examples/convert_to_faa.rs"
 
 [dependencies]
 clap = { version = "4.5.19", features = ["derive"] }

microBioRust/examples/src/blast_parse.rs → microBioRust/examples/blast_parse.rs

@@ -1,17 +1,15 @@
-use anyhow::{Context, Result};
-use async_compression::tokio::bufread::GzipDecoder as AsyncGzDecoder;
+use anyhow::Result;
 use clap::Parser;
-use quick_xml::events::Event;
-use quick_xml::reader::Reader;
-use quick_xml::escape::unescape;
-use serde::Serialize;
-use serde_json::ser::Serializer as JsonSerializer;
 use microBioRust::blast::*;
-use std::io::Cursor;
-use tokio::io::{self, AsyncBufRead, AsyncBufReadExt, AsyncRead, AsyncWriteExt, BufReader};
+use tokio::io::AsyncWriteExt;
 
 #[derive(Parser, Debug)]
-#[command(name = "blast-parsers", author, version, about = "async microBioRust BLAST parsers: for outfmt6 (single line tabular) and outfmt5 (xml)")]
+#[command(
+    name = "blast-parsers",
+    author,
+    version,
+    about = "async microBioRust BLAST parsers: for outfmt6 (single line tabular) and outfmt5 (xml)"
+)]
 struct Cli {
     ///Use .gz for gzip-compressed files.
     #[arg(short, long, default_value = "-")]
@@ -44,7 +42,11 @@ async fn main() -> Result<()> {
                         buf.push(b'\n');
                         tokio::io::stdout().write_all(&buf).await?;
                     } else {
-                        println!("query {:?} hits {}", iter_rec.query_def, iter_rec.hits.len());
+                        println!(
+                            "query {:?} hits {}",
+                            iter_rec.query_def,
+                            iter_rec.hits.len()
+                        );
                     }
                 }
                 Err(e) => eprintln!("xml parse error: {}", e),

microBioRust/examples/convert_to_faa.rs

@@ -0,0 +1,34 @@
+ use clap::Parser;
+ use std::{
+     fs::File,
+     io::{Write, BufWriter},
+ };
+ use microBioRust::{
+     genbank,
+ };
+
+ #[derive(Parser, Debug)]
+ #[clap(author, version, about)]
+ struct Arguments {
+ #[clap(short, long)]
+ filename: String,
+ #[clap(short, long)]
+ output: String,
+ }
+
+fn main() -> Result<(), anyhow::Error> {
+            let args = Arguments::parse();
+            let records = genbank!(&args.filename);
+            let file = File::create(&args.output)?;
+            let mut writer = BufWriter::new(file);
+            for record in records {
+               for (k, _v) in &record.cds.attributes {
+                  if let Some(seq) = record.seq_features.get_sequence_faa(k) {
+                     writeln!(writer, ">{}|{}\n{}", &record.id, &k, seq)?;
+                     }
+                  }
+            }
+            writer.flush()?;
+            Ok(())
+}
+

microBioRust/src/embl.rs

@@ -263,14 +263,14 @@
 //!```
 //!
 
-use anyhow::{anyhow, Context};
+use anyhow::{Context, anyhow};
 use bio::alphabets::dna::revcomp;
 use chrono::prelude::*;
 use lazy_static::lazy_static;
 use paste::paste;
 use protein_translate::translate;
-use serde::Serialize;
 use regex::Regex;
+use serde::Serialize;
 use std::{
     collections::{BTreeMap, HashSet},
     convert::{AsRef, TryInto},
@@ -600,8 +600,8 @@ where
                         //println!("designated codon start {:?} {:?}", &codon_start, &locus_tag);
                     }
                     if self.line_buffer.contains("/gene=") {
-                        let gen: Vec<&str> = self.line_buffer.split('\"').collect();
-                        gene = gen[1].to_string();
+                        let genes: Vec<&str> = self.line_buffer.split('\"').collect();
+                        gene = genes[1].to_string();
                         //println!("gene designated {:?} {:?}", &gene, &locus_tag);
                     }
                     if self.line_buffer.contains("/product") {
@@ -1542,7 +1542,7 @@ mod tests {
     #[allow(unused_assignments)]
     #[allow(unused_imports)]
     fn test_read_file() {
-        let content = std::fs::read_to_string("example.embl").expect("error reading file");
+        let content = std::fs::read_to_string("tests/example.embl").expect("error reading file");
         assert!(content.contains("ID"));
         assert!(content.len() > 0);
     }
@@ -1553,7 +1553,7 @@ mod tests {
     #[allow(unused_assignments)]
     #[allow(unused_imports)]
     fn test_parse_embl() {
-        let file_embl = "example.embl";
+        let file_embl = "tests/example.embl";
         let records = embl!(&file_embl);
         assert!(records.len() > 0);
     }
@@ -1564,7 +1564,7 @@ mod tests {
     #[allow(unused_assignments)]
     #[allow(unused_imports)]
     fn test_parse_source_attributes() {
-        let file_embl = "example.embl";
+        let file_embl = "tests/example.embl";
         let records = embl!(&file_embl);
         if let Some(record) = records.first() {
             if let Some((key, val)) = record.source_map.source_attributes.first_key_value() {
@@ -1579,7 +1579,7 @@ mod tests {
     #[allow(unused_assignments)]
     #[allow(unused_imports)]
     fn test_parse_cds_attributes() {
-        let file_embl = "example.embl";
+        let file_embl = "tests/example.embl";
         let records = embl!(&file_embl);
         if let Some(record) = records.first() {
             if let Some((locus_tag, vals)) = record.cds.attributes.first_key_value() {
@@ -1598,7 +1598,7 @@ mod tests {
     #[allow(unused_assignments)]
     #[allow(unused_imports)]
     fn test_parse_sequence_attributes() {
-        let file_embl = "example.embl";
+        let file_embl = "tests/example.embl";
         let records = embl!(&file_embl);
         if let Some(record) = records.first() {
             if let Some((key, vals)) = record.cds.attributes.first_key_value() {

microBioRust/src/gbk.rs

@@ -126,7 +126,7 @@
 //!        let mut read_counter: u32 = 0;
 //!        let mut seq_region: BTreeMap<String, (u32,u32)> = BTreeMap::new();
 //!        let mut record_vec: Vec<Record> = Vec::new();
-//!        loop {  
+//!        loop {
 //!            match records.next() {
 //!                Some(Ok(mut record)) => {
 //!	               println!("next record");
@@ -275,7 +275,7 @@
 //!```
 //!
 
-use anyhow::{anyhow, Context};
+use anyhow::{Context, anyhow};
 use bio::alphabets::dna::revcomp;
 use chrono::prelude::*;
 use itertools::Itertools;
@@ -681,8 +681,8 @@ where
                         //println!("designated codon start {:?} {:?}", &codon_start, &locus_tag);
                     }
                     if self.line_buffer.contains("/gene=") {
-                        let gen: Vec<&str> = self.line_buffer.split('\"').collect();
-                        gene = gen[1].to_string();
+                        let genes: Vec<&str> = self.line_buffer.split('\"').collect();
+                        gene = genes[1].to_string();
                         //println!("gene designated {:?} {:?}", &gene, &locus_tag);
                     }
                     if self.line_buffer.contains("/product") {
@@ -1732,7 +1732,7 @@ mod tests {
     #[allow(unused_assignments)]
     #[allow(unused_imports)]
     fn test_read_file() {
-        let content = std::fs::read_to_string("K12_ribo.gbk").expect("error reading file");
+        let content = std::fs::read_to_string("tests/K12_ribo.gbk").expect("error reading file");
         assert!(content.contains("LOCUS"));
         assert!(content.len() > 0);
     }
@@ -1743,7 +1743,7 @@ mod tests {
     #[allow(unused_assignments)]
     #[allow(unused_imports)]
     fn test_parse_gbk() {
-        let file_gbk = "K12_ribo.gbk";
+        let file_gbk = "tests/K12_ribo.gbk";
         let records = genbank!(&file_gbk);
         assert!(records.len() > 0);
     }
@@ -1754,7 +1754,7 @@ mod tests {
     #[allow(unused_assignments)]
     #[allow(unused_imports)]
     fn test_parse_source_attributes() {
-        let file_gbk = "K12_ribo.gbk";
+        let file_gbk = "tests/K12_ribo.gbk";
         let records = genbank!(&file_gbk);
         if let Some(record) = records.first() {
             if let Some((key, val)) = record.source_map.source_attributes.first_key_value() {
@@ -1769,7 +1769,7 @@ mod tests {
     #[allow(unused_assignments)]
     #[allow(unused_imports)]
     fn test_parse_cds_attributes() {
-        let file_gbk = "K12_ribo.gbk";
+        let file_gbk = "tests/K12_ribo.gbk";
         let records = genbank!(&file_gbk);
         if let Some(record) = records.first() {
             if let Some((locus_tag, vals)) = record.cds.attributes.first_key_value() {
@@ -1788,7 +1788,7 @@ mod tests {
     #[allow(unused_assignments)]
     #[allow(unused_imports)]
     fn test_parse_sequence_attributes() {
-        let file_gbk = "K12_ribo.gbk";
+        let file_gbk = "tests/K12_ribo.gbk";
         let records = genbank!(&file_gbk);
         if let Some(record) = records.first() {
             if let Some((key, vals)) = record.cds.attributes.first_key_value() {

microBioRust/tests/cleaned_dna.fasta

@@ -0,0 +1,6 @@
+>seq1
+ATGC-ATGCATGCATGC
+>seq2
+ATGCAATGCTTGCATGC
+>seq3
+TTGCAATCCATGCAAGC

microBioRust/tests/embl_to_faa.rs

@@ -2,7 +2,7 @@ use microBioRust::embl::Reader;
 use std::fs;
 #[test]
 fn embl_to_faa() -> Result<(), anyhow::Error> {
-    let file_embl = fs::File::open("example.embl")?;
+    let file_embl = fs::File::open("tests/example.embl")?;
     let reader = Reader::new(file_embl);
     let mut records = reader.records();
     let mut read_counter: u32 = 0;

microBioRust/tests/embl_to_ffn.rs

@@ -2,7 +2,7 @@ use microBioRust::embl::Reader;
 use std::fs;
 #[test]
 pub fn embl_to_ffn() -> Result<(), anyhow::Error> {
-    let file_embl = fs::File::open("example.embl")?;
+    let file_embl = fs::File::open("tests/example.embl")?;
     let reader = Reader::new(file_embl);
     let mut records = reader.records();
     let mut read_counter: u32 = 0;

microBioRust/tests/embl_to_gff.rs

@@ -1,10 +1,10 @@
-use microBioRust::embl::{gff_write, Reader, Record};
+use microBioRust::embl::{Reader, Record, gff_write};
 use std::collections::BTreeMap;
 use std::fs;
 
 #[test]
 fn test_embl_to_gff() -> std::io::Result<()> {
-    let file_embl = fs::File::open("example.embl")?;
+    let file_embl = fs::File::open("tests/example.embl")?;
     let reader = Reader::new(file_embl);
     let mut records = reader.records();
     let mut read_counter: u32 = 0;

microBioRust/tests/genbank_to_faa.rs

@@ -2,7 +2,7 @@ use microBioRust::gbk::Reader;
 use std::fs;
 #[test]
 pub fn genbank_to_faa() -> Result<(), anyhow::Error> {
-    let file_gbk = fs::File::open("K12_ribo.gbk")?;
+    let file_gbk = fs::File::open("tests/K12_ribo.gbk")?;
     let reader = Reader::new(file_gbk);
     let mut records = reader.records();
     let mut read_counter: u32 = 0;

microBioRust/tests/genbank_to_ffn.rs

@@ -2,7 +2,7 @@ use microBioRust::gbk::Reader;
 use std::fs;
 #[test]
 pub fn genbank_to_ffn() -> Result<(), anyhow::Error> {
-    let file_gbk = fs::File::open("K12_ribo.gbk")?;
+    let file_gbk = fs::File::open("tests/K12_ribo.gbk")?;
     let reader = Reader::new(file_gbk);
     let mut records = reader.records();
     let mut read_counter: u32 = 0;

microBioRust/tests/genbank_to_gff.rs

@@ -1,10 +1,10 @@
-use microBioRust::gbk::{gff_write, Reader, Record};
+use microBioRust::gbk::{Reader, Record, gff_write};
 use std::collections::BTreeMap;
 use std::fs;
 use std::io;
 #[test]
 pub fn genbank_to_gff() -> io::Result<()> {
-    let file_gbk = fs::File::open("K12_ribo.gbk")?;
+    let file_gbk = fs::File::open("tests/K12_ribo.gbk")?;
     let _prev_start: u32 = 0;
     let mut prev_end: u32 = 0;
     let reader = Reader::new(file_gbk);

microBioRust/tests/new_output_embl.gbk

@@ -0,0 +1,52 @@
+LOCUS       source_1             928 bp    DNA     linear CON 01-JUN-2026
+DEFINITION  Escherichia coli K-12 substr. MG1655.
+ACCESSION   source_1
+KEYWORDS    .
+SOURCE      Escherichia coli K-12 substr. MG1655
+  ORGANISM  Escherichia coli K-12 substr. MG1655
+FEATURES             Location/Qualifiers
+     source          1..910
+                     /organism="K-12 substr. MG1655"
+                     /mol_type="DNA"
+                     /strain="K-12 substr. MG1655"
+                     /db_xref="PRJNA57779"
+     gene            complement(1..354)
+                     /locus_tag="b3304"
+     CDS             complement(1..354)
+                     /locus_tag="b3304"
+                     /codon_start="1"
+                     /gene="rplR"
+                     /translation="MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGS
+                     LVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRVQAL
+                     DAAREAGLQ"
+                     /product="50S ribosomal subunit protein L18"
+     gene            complement(364..897)
+                     /locus_tag="b3305"
+     CDS             complement(364..897)
+                     /locus_tag="b3305"
+                     /codon_start="1"
+                     /gene="rplF"
+                     /translation="MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKH
+                     NTLTFGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLS
+                     GFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYAD
+                     VVRTKEAKK"
+                     /product="50S ribosomal subunit protein L6"
+ORIGIN
+    1 acctctacct tagaactgaa ggccagcttc acgggcagca tctgccagtg cctggacacg
+   61 accatgatat tggaacccgg aacggtcaaa ggatacatct ttgatgcctt tttccagagc
+  121 gcgttcagcg acagctttac ccacagctgc agccgcgtct ttgttaccgg tgtacttcag
+  181 ttgttcagcg atagcttttt ctacagtaga agcagctacc agaacttcag aaccgttcgg
+  241 tgcaattacc tgtgcgtaaa tgtgacgcgg ggtacgatgt accaccaggc gagttgcgcc
+  301 cagctcctgg agcttgcggc gtgcgcgggt cgcacgacgg atacgagcag atttcttatc
+  361 catagtgtta ccttacttct tcttagcctc tttggtacgc acgacttcgt cggcgtaacg
+  421 aacacccttg cctttataag gctcaggacg acggtaggcg cgcagatccg ctgcaacctg
+  481 gccgatcacc tgcttatcag cgcctttcag cacgatttca gtctgagtcg gacattcagc
+  541 agtgataccc gcaggcagct gatggtcaac aggatgagag aaacccagag acaggttaat
+  601 cacattgcct ttaaccgctg cacggtaacc tacaccaacc agctgcagct tcttagtgaa
+  661 gccttcggta acaccgataa ccattgagtt cagcagggca cgcgcggtac cagcctgtgc
+  721 ccaaccgtct gcgtaaccat cacgcggacc gaaggtcagg gtattatctg catgtttaac
+  781 ttcaacagca tcgttgagag tacgagtcag ctcgccgttt ttacctttga tcgtaataac
+  841 ctgaccgttg atttttacgt caacgccggc aggaacaacg accggtgctt tagcaacacg
+  901 agacattttt tcc
+
+//