kseq 0.5.3

a simple fasta/fastq format parser library
Documentation 
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use kseq;
use std::io::Cursor;
use std::result::Result;

// https://stackoverflow.com/questions/53124930/how-do-you-test-for-a-specific-rust-error
macro_rules! assert_err {
    ($expression:expr, $($pattern:tt)+) => {
        match $expression {
            $($pattern)+ => (),
            ref e => panic!("expected `{}` but got `{:?}`", stringify!($($pattern)+), e),
        }
    }
}

fn count_base(input: Vec<u8>) -> Result<usize, kseq::record::ParseError> {
    let mut len_bases = 0;
    let mut seq_bases = 0;
    let mut records = kseq::parse_reader(Cursor::new(input))?;
    while let Some(record) = records.iter_record()? {
        len_bases += record.len();
        seq_bases += record.seq().len();
    }
    assert_eq!(len_bases, seq_bases);
    Ok(len_bases)
}

static BASE_SEQ: &str = "ATGCATGCATGC";
static BASE_QUAL: &str = "@@@@@@@@@@@@";

#[test]
fn test_normal_one_line_fasta() {
    let data: Vec<u8> =
        format!(">1 record1\n{seq}\n>2 record2\n{seq}", seq = BASE_SEQ).into_bytes();
    assert_eq!(BASE_SEQ.len() * 2, count_base(data).unwrap());
}

#[test]
fn test_normal_one_line_fastq() {
    let data: Vec<u8> = format!(
        "@1 record1\n{seq}\n+\n{qual}\n@2 record2\n{seq}\n+\n{qual}",
        seq = BASE_SEQ,
        qual = BASE_QUAL
    )
    .into_bytes();
    assert_eq!(BASE_SEQ.len() * 2, count_base(data).unwrap());
}

#[test]
fn test_normal_multi_line_fasta() {
    let data: Vec<u8> = format!(
        ">1 record1\n{seq}\n{seq}\n>2 record2\n{seq}\n{seq}",
        seq = BASE_SEQ
    )
    .into_bytes();
    assert_eq!(BASE_SEQ.len() * 4, count_base(data).unwrap());
}

#[test]
fn test_normal_multi_line_fastq() {
    let data: Vec<u8> = format!(
        "@1 record1\n{seq}\n{seq}\n+\n{qual}\n{qual}\n@2 record2\n{seq}\n{seq}\n+\n{qual}{qual}\n",
        seq = BASE_SEQ,
        qual = BASE_QUAL
    )
    .into_bytes();
    assert_eq!(BASE_SEQ.len() * 4, count_base(data).unwrap());
}

#[test]
fn test_truncate_fasta_miss_head() {
    let data: Vec<u8> = format!(">1 record1\n{seq}\n>", seq = BASE_SEQ).into_bytes();
    assert_err!(
        count_base(data),
        Err(kseq::record::ParseError::TruncateFile(_))
    );
}

#[test]
fn test_truncate_fasta_miss_seq() {
    let data: Vec<u8> = format!(">1 record1\n{seq}{seq}\n>2 record2", seq = BASE_SEQ).into_bytes();
    assert_err!(
        count_base(data),
        Err(kseq::record::ParseError::TruncateFile(_))
    );
}

#[test]
fn test_truncate_fastq_miss_head() {
    let data: Vec<u8> = format!(
        "@1 record1\n{seq}{seq}\n+\n{qual}{qual}\n@\n",
        seq = BASE_SEQ,
        qual = BASE_QUAL
    )
    .into_bytes();
    assert_err!(
        count_base(data),
        Err(kseq::record::ParseError::TruncateFile(_))
    );
}

#[test]
fn test_truncate_fastq_miss_seq() {
    let data: Vec<u8> = format!("@1 record1").into_bytes();
    assert_err!(
        count_base(data),
        Err(kseq::record::ParseError::TruncateFile(_))
    );
}

#[test]
fn test_truncate_fastq_miss_sep() {
    let data: Vec<u8> = format!("@1 record1\n{seq}{seq}", seq = BASE_SEQ).into_bytes();
    assert_err!(
        count_base(data),
        Err(kseq::record::ParseError::TruncateFile(_))
    );
}

#[test]
fn test_truncate_fastq_miss_qual() {
    let data: Vec<u8> = format!("@1 record1\n{seq}{seq}\n+", seq = BASE_SEQ).into_bytes();
    assert_err!(
        count_base(data),
        Err(kseq::record::ParseError::TruncateFile(_))
    );
}

#[test]
fn test_invalid_fasta_miss_head() {
    let data: Vec<u8> = format!(">\n{seq}\n>2 record2\n{seq}", seq = BASE_SEQ).into_bytes();
    assert_err!(
        count_base(data),
        Err(kseq::record::ParseError::InvalidFasta(_))
    );
}

#[test]
fn test_invalid_fasta_miss_seq() {
    let data: Vec<u8> = format!(">1 record1\n\n>2 record2\n{seq}", seq = BASE_SEQ).into_bytes();
    assert_err!(
        count_base(data),
        Err(kseq::record::ParseError::InvalidFasta(_))
    );
}

#[test]
fn test_invalid_fasta_with_seq_len_is_0() {
    let data: Vec<u8> = format!(">1 record1\n{seq}\n>2 record2\n{seq}", seq = "").into_bytes();
    assert_err!(
        count_base(data),
        Err(kseq::record::ParseError::InvalidFasta(_))
    );
}

#[test]
fn test_invalid_fastq_miss_head() {
    let data: Vec<u8> = format!(
        "@\n{seq}{seq}\n+\n{qual}{qual}\n@2 record2\n{seq}{seq}\n+\n{qual}{qual}\n",
        seq = BASE_SEQ,
        qual = BASE_QUAL
    )
    .into_bytes();
    assert_err!(
        count_base(data),
        Err(kseq::record::ParseError::InvalidFastq(_))
    );
}

#[test]
fn test_invalid_fastq_miss_seq() {
    let data: Vec<u8> = format!(
        "@1 record1\n{qual}{qual}\n@2 record2\n{seq}{seq}\n+\n{qual}{qual}\n",
        seq = BASE_SEQ,
        qual = BASE_QUAL
    )
    .into_bytes();
    assert_err!(
        count_base(data),
        Err(kseq::record::ParseError::InvalidFastq(_))
    );
}

#[test]
fn test_invalid_fastq_miss_sep() {
    let data: Vec<u8> = format!(
        "@1 record1\n{seq}{seq}\n{qual}{qual}\n@2 record2\n{seq}{seq}\n+\n{qual}{qual}\n",
        seq = BASE_SEQ,
        qual = BASE_QUAL
    )
    .into_bytes();
    assert_err!(
        count_base(data),
        Err(kseq::record::ParseError::InvalidFastq(_))
    );
}

#[test]
fn test_invalid_fastq_miss_qual() {
    let data: Vec<u8> = format!(
        "@1 record1\n{seq}{seq}\n@2 record2\n{seq}{seq}\n+\n{qual}{qual}\n",
        seq = BASE_SEQ,
        qual = BASE_QUAL
    )
    .into_bytes();
    assert_err!(
        count_base(data),
        Err(kseq::record::ParseError::InvalidFastq(_))
    );
}


#[test]
fn test_invalid_fastq_seq_has_diff_len_with_qual() {
    let data: Vec<u8> = format!(
        "@1 record1\n{seq}{seq}\n+\n{qual}{qual}\n@2 record2\n{seq}{seq}\n+\n{qual}{qual}\n",
        seq = BASE_SEQ,
        qual = &BASE_QUAL[0..BASE_SEQ.len() - 1]
    )
    .into_bytes();
    assert_err!(
        count_base(data),
        Err(kseq::record::ParseError::InvalidFastx(_))
    );
}

#[test]
fn test_invalid_fastq_with_seq_len_is_0() {
    let data: Vec<u8> = format!(
        "@1 record1\n{seq}\n+\n{qual}\n@2 record2\n{seq}\n+\n{qual}\n",
        seq = "",
        qual = ""
    )
    .into_bytes();
    assert_err!(
        count_base(data),
        Err(kseq::record::ParseError::InvalidFastq(_))
    );
}

// #[test]
// fn test_large_fasta() {
//     let count = 1_000_000;
//     let mut total_len = 0;
//     let mut data = Vec::with_capacity(count * 20);
//     (0..count).for_each(|x| {
//         writeln!(&mut data, ">{x} record{x}\n").expect("Failed to write to Vec");
//         (0..count & 0xff).for_each(|_| {
//             total_len += BASE_SEQ.len();
//             writeln!(&mut data, "{BASE_SEQ}").expect("Failed to write to Vec");
//         });
//         writeln!(&mut data, "\n").expect("Failed to write to Vec");
//     });

//     assert_eq!(count_base(data).unwrap(), total_len);
// }

// #[test]
// fn test_large_fastq() {
//     let count = 1_000_000;
//     let mut total_len = 0;
//     let mut data = Vec::with_capacity(count * 20);
//     (0..count).for_each(|x| {
//         writeln!(&mut data, "@{x} record{x}\n").expect("Failed to write to Vec");
//         (0..count & 0xff).for_each(|_| {
//             total_len += BASE_SEQ.len();
//             writeln!(&mut data, "{BASE_SEQ}").expect("Failed to write to Vec");
//         });
//         writeln!(&mut data, "\n+\n").expect("Failed to write to Vec");
//         (0..count & 0xff).for_each(|_| {
//             writeln!(&mut data, "{BASE_QUAL}").expect("Failed to write to Vec");
//         });
//         writeln!(&mut data, "\n").expect("Failed to write to Vec");
//     });

//     assert_eq!(count_base(data).unwrap(), total_len);
// }