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LCrossmanLCrossman
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exporting align and blast parsers to microbiorust-py
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Lines changed: 6138 additions & 85 deletions

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‎microBioRust/examples/src/blast_parse.rs‎

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use anyhow::{Context, Result};
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use async_compression::tokio::bufread::GzipDecoder as AsyncGzDecoder;
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use clap::Parser;
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use quick_xml::events::Event;
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use quick_xml::reader::Reader;
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use quick_xml::escape::unescape;
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use serde::Serialize;
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use serde_json::ser::Serializer as JsonSerializer;
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use microBioRust::blast::*;
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use std::io::Cursor;
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use tokio::io::{self, AsyncBufRead, AsyncBufReadExt, AsyncRead, AsyncWriteExt, BufReader};
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#[derive(Parser, Debug)]
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#[command(name = "blast-parsers", author, version, about = "async microBioRust BLAST parsers: for outfmt6 (single line tabular) and outfmt5 (xml)")]
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struct Cli {
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///Use .gz for gzip-compressed files.
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#[arg(short, long, default_value = "-")]
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input: String,
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/// Format: '6' (tabular) or '5' (xml). If omitted we try to infer by file suffix only
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#[arg(short, long)]
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format: Option<String>,
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/// Output newline-delimited JSON (one JSON object per record/iteration)
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#[arg(long)]
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json: bool,
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}
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#[tokio::main]
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async fn main() -> Result<()> {
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let args = Cli::parse();
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let fmt = infer_format(&args.input, &args.format);
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let reader_box = open_async_reader(&args.input).await?;
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if fmt == "6" {
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stream_outfmt6_to_json(reader_box).await?;
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} else {
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// Build AsyncBlastXmlIter from reader_box
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let iter_reader = reader_box;
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let mut iter = AsyncBlastXmlIter::from_reader(iter_reader);
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while let Some(res) = iter.next_iteration().await {
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match res {
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Ok(iter_rec) => {
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if args.json {
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let mut buf = Vec::new();
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serde_json::to_writer(&mut buf, &iter_rec)?;
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buf.push(b'\n');
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tokio::io::stdout().write_all(&buf).await?;
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} else {
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println!("query {:?} hits {}", iter_rec.query_def, iter_rec.hits.len());
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}
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}
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Err(e) => eprintln!("xml parse error: {}", e),
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}
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}
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}
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Ok(())
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}

‎microBioRust/src/blast.rs‎

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@@ -97,7 +97,6 @@
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#![allow(unused_imports)]
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use anyhow::{Context, Result};
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use async_compression::tokio::bufread::GzipDecoder as AsyncGzDecoder;
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use clap::Parser;
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use quick_xml::events::Event;
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use quick_xml::reader::Reader;
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use quick_xml::escape::unescape;
@@ -173,11 +172,11 @@ pub struct Statistics {
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// first macro: For Option fields (Strings, Option<u32>, etc.)
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macro_rules! read_parse_opt {
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($self:expr, $tag:expr, $parent_opt:expr, $field:ident, $ok_ty:ty) => {{
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// 1. Read the content first. This borrows 'self', but the borrow ends
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// as soon as this statement finishes.
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//read content first. This borrows 'self', but the borrow ends
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//as soon as this statement finishes.
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let res = $self.read_tag_content($tag).await;
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// 2. Now 'self' is free again. We can handle the result.
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//now 'self' is free again and we can handle the result.
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match res {
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Ok(text) => {
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// 3. Re-borrow only the specific field we want to update.
@@ -566,58 +565,29 @@ where
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}
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//here we use input in a format such as this in order to capture the required format of XML (5) or Tabular (6) and true or false for Json output
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//see examples for further detail
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570-
#[derive(Parser, Debug)]
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#[command(name = "blast-parsers", author, version, about = "async microBioRust BLAST parsers: for outfmt6 (single line tabular) and outfmt5 (xml)")]
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struct Cli {
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///Use .gz for gzip-compressed files.
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#[arg(short, long, default_value = "-")]
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input: String,
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/// Format: '6' (tabular) or '5' (xml). If omitted we try to infer by file suffix only
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#[arg(short, long)]
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format: Option<String>,
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/// Output newline-delimited JSON (one JSON object per record/iteration)
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#[arg(long)]
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json: bool,
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}
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//#[derive(Parser, Debug)]
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//#[command(name = "blast-parsers", author, version, about = "async microBioRust BLAST parsers: for outfmt6 (single line tabular) and outfmt5 (xml)")]
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//struct Cli {
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// ///Use .gz for gzip-compressed files.
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// #[arg(short, long, default_value = "-")]
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// input: String,
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// /// Format: '6' (tabular) or '5' (xml). If omitted we try to infer by file suffix only
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// #[arg(short, long)]
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// format: Option<String>,
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// /// Output newline-delimited JSON (one JSON object per record/iteration)
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// #[arg(long)]
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// json: bool,
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//}
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584-
fn infer_format(path: &str, explicit: &Option<String>) -> String {
585+
pub fn infer_format(path: &str, explicit: &Option<String>) -> String {
585586
if let Some(f) = explicit { return f.clone(); }
586587
if path.ends_with(".xml") || path.ends_with(".xml.gz") { "5".to_string() }
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else { "6".to_string() }
588589
}
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590-
#[tokio::main]
591-
async fn main() -> Result<()> {
592-
let args = Cli::parse();
593-
let fmt = infer_format(&args.input, &args.format);
594-
let reader_box = open_async_reader(&args.input).await?;
595-
if fmt == "6" {
596-
stream_outfmt6_to_json(reader_box).await?;
597-
} else {
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// Build AsyncBlastXmlIter from reader_box
599-
let iter_reader = reader_box;
600-
let mut iter = AsyncBlastXmlIter::from_reader(iter_reader);
601-
while let Some(res) = iter.next_iteration().await {
602-
match res {
603-
Ok(iter_rec) => {
604-
if args.json {
605-
let mut buf = Vec::new();
606-
serde_json::to_writer(&mut buf, &iter_rec)?;
607-
buf.push(b'\n');
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tokio::io::stdout().write_all(&buf).await?;
609-
} else {
610-
println!("query {:?} hits {}", iter_rec.query_def, iter_rec.hits.len());
611-
}
612-
}
613-
Err(e) => eprintln!("xml parse error: {}", e),
614-
}
615-
}
616-
}
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618-
Ok(())
619-
}
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// Unit tests (async if relevant)
622592
#[cfg(test)]
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mod tests {

‎microBioRust/tests/data/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/tests/data/cleaned_dna.fasta‎

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>seq1
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ATGC-ATGCATGCATGC
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>seq2
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ATGCAATGCTTGCATGC
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>seq3
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TTGCAATCCATGCAAGC

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