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+use std::io; +use std::process::exit; +use std::thread; + +use std::time; + +use std::sync::mpsc::sync_channel; + +#[cfg(feature = "mzmlb")] +use mzdata::io::mzmlb; + +use mzdata::io::{ + infer_format, infer_from_path, infer_from_stream, + MassSpectrometryFormat, PreBufferedStream, +}; +use mzdata::prelude::*; +use mzdata::{MGFReader, MGFWriter, MzMLReader, MzMLWriter}; + +#[derive(Debug, Clone)] +pub struct MZConvert { + pub inpath: String, + pub outpath: String, +} + +impl MZConvert { + pub fn new(inpath: String, outpath: String) -> Self { + Self { inpath, outpath } + } + + pub fn main(&self) -> io::Result<()> { + self.reader_then() + } + + fn reader_then(&self) -> io::Result<()> { + if self.inpath == "-" { + let mut stream = PreBufferedStream::new(io::stdin())?; + let (ms_format, _compressed) = infer_from_stream(&mut stream)?; + match ms_format { + MassSpectrometryFormat::MGF => self.writer_then(MGFReader::new(stream))?, + MassSpectrometryFormat::MzML => self.writer_then(MzMLReader::new(io::BufReader::new(stream)))?, + _ => { + eprintln!("Could not infer input format from STDIN"); + exit(1) + } + } + } else { + let (ms_format, _compressed) = infer_format(&self.inpath)?; + match ms_format { + MassSpectrometryFormat::MGF => { + let reader = MGFReader::open_path(&self.inpath)?; + self.writer_then(reader)?; + } + MassSpectrometryFormat::MzML => { + let reader = MzMLReader::open_path(&self.inpath)?; + self.writer_then(reader)?; + } + #[cfg(feature = "mzmlb")] + MassSpectrometryFormat::MzMLb => { + let reader = mzmlb::MzMLbReader::open_path(&self.inpath)?; + self.writer_then(reader)?; + } + _ => { + eprintln!("Could not infer input format from {}", self.inpath); + exit(1) + } + } + }; + Ok(()) + } + + fn writer_then( + &self, + reader: R, + ) -> io::Result<()> { + match infer_from_path(&self.outpath).0 { + MassSpectrometryFormat::MGF => { + let writer = MGFWriter::new(io::BufWriter::new(fs::File::create(&self.outpath)?)); + self.task(reader, writer)?; + } + MassSpectrometryFormat::MzML => { + let mut writer = + MzMLWriter::new(io::BufWriter::new(fs::File::create(&self.outpath)?)); + writer.copy_metadata_from(&reader); + self.task(reader, writer)?; + } + #[cfg(feature = "mzmlb")] + MassSpectrometryFormat::MzMLb => { + let mut writer = mzmlb::MzMLbWriterBuilder::new(&self.outpath) + .with_zlib_compression(9) + .create()?; + writer.copy_metadata_from(&reader); + self.task(reader, writer)?; + } + _ => { + eprintln!("Could not infer output format from {}", self.outpath); + exit(1) + } + } + Ok(()) + } + + fn task + Send + 'static>( + &self, + reader: R, + mut writer: W, + ) -> io::Result<()> { + let (send, recv) = sync_channel(2usize.pow(16)); + + let reader_handle = thread::spawn(move || { + reader.for_each(|s| send.send(s).unwrap()); + }); + + let writer_handle = thread::spawn(move || { + for s in recv.iter() { + writer.write(&s).unwrap(); + } + writer.close().unwrap(); + }); + + reader_handle.join().unwrap(); + writer_handle.join().unwrap(); + Ok(()) + } +} + +fn main() -> io::Result<()> { + let inpath = env::args().nth(1).unwrap_or_else(|| { + eprintln!("Please provide a path to read an MS data file from, or '-'"); + exit(1) + }); + + let outpath = env::args().nth(2).unwrap_or_else(|| { + eprintln!("Please provide a path to write an MS file to, or '-'"); + exit(1) + }); + + let start = time::Instant::now(); + let job = MZConvert::new(inpath, outpath); + job.main()?; + let end = time::Instant::now(); + let elapsed = end - start; + eprintln!("Conversion finished: {:0.2} seconds", elapsed.as_secs_f64()); + Ok(()) +} diff --git a/src/io/mgf.rs b/src/io/mgf.rs index 1071706..65983a2 100644 --- a/src/io/mgf.rs +++ b/src/io/mgf.rs @@ -726,7 +726,8 @@ impl< fn write_param(&mut self, param: &P) -> io::Result<()> { self.handle - .write_all(param.name().to_uppercase().as_bytes())?; + .write_all(param.name().to_uppercase().replace(" ", "_").as_bytes())?; + self.handle.write_all(b"=")?; self.handle.write_all(param.value().as_bytes())?; self.handle.write_all(b"\n")?; Ok(()) @@ -781,9 +782,7 @@ TITLE="#, None => {} } for param in desc.params() { - self.handle - .write_all(param.name.to_uppercase().as_bytes())?; - self.handle.write_all(param.value.as_bytes())?; + self.write_param(param)?; } Ok(())