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use std::fs;
use needletail::errors::ParseError;
use needletail::parser::parse_fastx_file;
use serde_derive::Deserialize;
#[derive(Debug, Deserialize)]
struct TestCase {
filename: String,
// origin: String,
tags: Option<Vec<String>>,
// comments: Option<Vec<String>>,
}
#[derive(Debug, Deserialize)]
struct TestIndex {
valid: Vec<TestCase>,
invalid: Option<Vec<TestCase>>,
}
fn test_fastx_file(path: &str) -> Result<(), ParseError> {
let mut reader = parse_fastx_file(path)?;
while let Some(rec) = reader.next() {
let _ = rec?;
}
Ok(())
}
#[test]
fn test_specimen_fasta() {
let raw_index = fs::read_to_string("tests/specimen/FASTA/index.toml").unwrap();
let index: TestIndex = toml::from_str(&raw_index).expect("Could not deserialize index");
for test in index.valid {
// what kind of sicko puts comments in FASTAs?
if test
.tags
.unwrap_or_else(Vec::new)
.contains(&String::from("comments"))
{
continue;
}
let path = format!("tests/specimen/FASTA/{}", test.filename);
assert_eq!(test_fastx_file(&path), Ok(()));
}
}
#[test]
fn test_specimen_fastq() {
let raw_index = fs::read_to_string("tests/specimen/FASTQ/index.toml").unwrap();
let index: TestIndex = toml::from_str(&raw_index).expect("Could not deserialize index");
for test in index.valid {
if test.filename == "wrapping_original_sanger.fastq"
|| test.filename == "longreads_original_sanger.fastq"
|| test.filename == "tricky.fastq"
{
// may god have mercy upon us if someone ever tries a file like this
// (sequences are one-line, but quality scores are line-wrapped)
continue;
}
let path = format!("tests/specimen/FASTQ/{}", test.filename);
assert!(
test_fastx_file(&path).is_ok(),
"File {} is bad?",
test.filename
);
}
for test in index.invalid.unwrap_or_default() {
if test.filename == "error_diff_ids.fastq" {
// we don't care if the sequence ID doesn't match the quality id?
continue;
}
// We don't check for ascii validity since it's a big hit perf wise
// This means some invalid sequences are considered ok but it's not a big issue
// in practice
if test.filename.starts_with("error_qual_")
|| test.filename == "error_spaces.fastq"
|| test.filename == "error_tabs.fastq"
{
continue;
}
let path = format!("tests/specimen/FASTQ/{}", test.filename);
assert!(
test_fastx_file(&path).is_err(),
"File {} is good?",
test.filename
);
}
}
|
