[DO NOT MERGE] Parsing Phylogenetic trees

Cargo.toml

@@ -2,7 +2,7 @@
 members = [
    "microBioRust",
    "heatmap",
-   "seqmetrics"]
+   "seqmetrics", "phylo"]
 resolver = "2"
 
 [profile.dev]

microBioRust/cleaned_dna.fasta

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

microBioRust/new_output_embl.gbk

@@ -0,0 +1,104 @@
+LOCUS       source_1             928 bp    DNA     linear CON 20-OCT-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
+
+//
+LOCUS       source_1             928 bp    DNA     linear CON 20-OCT-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
+
+//

phylo/Cargo.toml

@@ -0,0 +1,20 @@
+[package]
+name = "microBioRust-phylo"
+license = "MIT"
+keywords = ["bioinformatics","micro","bio","genomics","sequence-analysis"]
+description = "Microbiology friendly bioinformatics Rust functions"
+categories = ["science::bioinformatics::sequence-analysis", "science::bioinformatics::genomics", "science::bioinformatics","visualization","data-structures"]
+readme = "README.md"
+exclude = [".git",".gitignore"]
+repository = "https://github.com/LCrossman/microBioRust"
+version = "0.1.0"
+edition = "2024"
+
+[lib]
+crate-type = ["cdylib"]
+
+[package.metadata.wasm-pack.profile.release]
+opt-level = "z"
+
+[dependencies]
+phylo = "6.0.0"

phylo/src/lib.rs

@@ -0,0 +1,11 @@
+/*!
+ The aim of this crate is to provide Microbiology friendly Rust functions for bioinformatics.
+
+ With phylo module you should be able to
+
+ 1. Parse newick trees into Rust equivalent data structure
+ 2. Conversion of newick tree format to other file formats like phyloXML
+ 3. Neighbor joining, bootstrapping from many files, visualizing, rooting etc.
+*/
+#![allow(non_snake_case)]
+pub mod parser;

phylo/src/parser.rs

@@ -0,0 +1,126 @@
+use std::io::{BufRead, Error, ErrorKind};
+
+use phylo::prelude::*;
+
+struct Scanner<R: BufRead> {
+    col: usize,
+    line: usize,
+    reader: R,
+    scratch: Vec<u8>,
+}
+
+impl<R: BufRead> Scanner<R> {
+    fn new(reader: R) -> Self {
+        Self {
+            reader,
+            line: 1,
+            col: 0,
+            scratch: vec![],
+        }
+    }
+}
+
+impl<R: BufRead> Iterator for Scanner<R> {
+    type Item = std::io::Result<Vec<u8>>;
+
+    fn next(&mut self) -> Option<Self::Item> {
+        loop {
+            let buffer = self.reader.fill_buf().ok()?;
+            let mut consumed_amt = 0;
+            let mut flush = false;
+            let buffer_len = buffer.len();
+
+            if buffer.is_empty() {
+                if self.scratch.is_empty() {
+                    return None; // reached EOF without any issues
+                } else {
+                    return Some(Err(Error::new(
+                        ErrorKind::InvalidData,
+                        format!(
+                            "Incomplete newick tree found at line: {}, col:{}",
+                            self.line, self.col
+                        ),
+                    )));
+                }
+            }
+
+            while consumed_amt < buffer_len {
+                let b = buffer[consumed_amt];
+                consumed_amt += 1;
+
+                if b == b'\n' {
+                    self.line += 1;
+                    self.col = 0;
+                } else {
+                    self.col += 1;
+                }
+
+                if b.is_ascii_whitespace() {
+                    continue;
+                }
+                self.scratch.push(b);
+                if b == b';' {
+                    flush = true;
+                    break;
+                }
+            }
+            self.reader.consume(consumed_amt);
+            if flush {
+                return Some(Ok(std::mem::take(&mut self.scratch)));
+            }
+        }
+    }
+}
+
+struct PhyloParser<R: BufRead> {
+    scanner: Scanner<R>,
+}
+
+impl<R: BufRead> PhyloParser<R> {
+    fn new(scanner: Scanner<R>) -> Self {
+        Self { scanner }
+    }
+}
+
+impl<R: BufRead> Iterator for PhyloParser<R> {
+    type Item = std::io::Result<PhyloTree>;
+
+    fn next(&mut self) -> Option<Self::Item> {
+        let bytes = match self.scanner.next()? {
+            Ok(b) => b,
+            Err(e) => return Some(Err(e)),
+        };
+        Some(
+            PhyloTree::from_newick(&bytes)
+                .map_err(|e| Error::new(ErrorKind::InvalidData, e.to_string())),
+        )
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use std::{fs::File, io::BufReader};
+
+    use super::*;
+
+    fn get_scanner(file_name: &str) -> Scanner<BufReader<File>> {
+        let path = format!("{}/tests/data/{}", env!("CARGO_MANIFEST_DIR"), file_name);
+        let file_handle = File::open(path).unwrap();
+        Scanner::new(BufReader::new(file_handle))
+    }
+
+    #[test]
+    fn test_scanner_newick_multitree_file() {
+        let mut scanner = get_scanner("basic_trees.nw");
+        let first_tree = scanner.next().unwrap().unwrap();
+        assert_eq!(String::from_utf8(first_tree).unwrap(), "(,,(,));")
+    }
+
+    #[test]
+    fn test_basic_parsing() {
+        let scanner = get_scanner("basic_trees.nw");
+        let mut parser = PhyloParser::new(scanner);
+        let first_tree = parser.next().unwrap().unwrap();
+        assert_eq!(first_tree.to_newick().to_string(), "(,,(,));");
+    }
+}

phylo/tests/data/basic_trees.nw

@@ -0,0 +1,8 @@
+(,,(,));
+(A,B,(C,D));
+(A,B,(C,D)E)F;
+(:0.1,:0.2,(:0.3,:0.4):0.5);
+(:0.1,:0.2,(:0.3,:0.4):0.5):0.0;
+(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);
+(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;
+((B:0.2,(C:0.3,D:0.4)E:0.5)F:0.1)A;