Function fastx::FastX::reader_from_path
source · Examples found in repository?
examples/fastx_cat.rs (line 12)
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fn main() -> io::Result<()>
{
for filename in args().skip(1)
{
println!("{}", filename);
let mut fastx_reader = FastX::reader_from_path(Path::new(&filename))?;
let mut fastx_record = FastX::from_reader(&mut fastx_reader)?;
while let Ok(_some @ 1..=usize::MAX) = fastx_record.read(&mut fastx_reader)
{
println!(">{} {}\n{}", fastx_record.id(), fastx_record.desc(), String::from_utf8_lossy(&fastx_record.seq()));
}
}
Ok(())
}
More examples
examples/fastq_cat.rs (line 13)
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fn main() -> io::Result<()>
{
for filename in args().skip(1)
{
println!("{}", filename);
let mut fastx_reader = FastX::reader_from_path(Path::new(&filename))?;
let mut fastq_record = FastX::FastQRecord::default();
while let Ok(_some @ 1..=usize::MAX) = fastq_record.read(&mut fastx_reader)
{
println!("@{} {}\n{}\n+{}\n{}",
fastq_record.id(),
fastq_record.desc(),
String::from_utf8_lossy(&fastq_record.seq()),
fastq_record.comment(),
String::from_utf8_lossy(&fastq_record.qual()));
}
}
Ok(())
}
examples/fastx_count.rs (line 12)
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fn main() -> io::Result<()>
{
for filename in args().skip(1)
{
println!("{}", filename);
let mut fastx_reader = FastX::reader_from_path(Path::new(&filename))?;
let mut fastx_record = FastX::from_reader(&mut fastx_reader)?;
/*
// just for fun read the first line and seek back
use std::io::BufRead;
let mut line = String::new();
let offset = fastx_reader.read_line(&mut line)?;
println!("{}", line);
fastx_reader.seek_relative(- (offset as i64))?;
*/
// back to serious processing
while let Ok(_some @ 1..=usize::MAX) = fastx_record.read(&mut fastx_reader)
{
println!("{}\t{}", fastx_record.id(), fastx_record.seq_len())
}
}
Ok(())
}