from __future__ import annotations

import importlib.util
import sys
from pathlib import Path


SCRIPT = Path(__file__).resolve().parents[2] / "scripts" / "check_rnaseq_strandness.py"


def load_module():
    assert SCRIPT.exists(), f"Missing script: {SCRIPT}"
    spec = importlib.util.spec_from_file_location("check_rnaseq_strandness", SCRIPT)
    assert spec and spec.loader
    module = importlib.util.module_from_spec(spec)
    sys.modules[spec.name] = module
    spec.loader.exec_module(module)
    return module


def test_discovers_paired_fastqs(tmp_path):
    module = load_module()
    for name in ["S1_1.fastq.gz", "S1_2.fastq.gz", "S2_R1.fq.gz", "S2_R2.fq.gz"]:
        (tmp_path / name).write_text("")

    pairs = module.discover_fastq_pairs(tmp_path)

    assert [p.sample for p in pairs] == ["S1", "S2"]
    assert pairs[0].r1.name == "S1_1.fastq.gz"
    assert pairs[0].r2.name == "S1_2.fastq.gz"
    assert pairs[1].r1.name == "S2_R1.fq.gz"
    assert pairs[1].r2.name == "S2_R2.fq.gz"


def test_gtf_conversion_writes_bed12(tmp_path):
    module = load_module()
    gtf = tmp_path / "genes.gtf"
    bed = tmp_path / "genes.bed12"
    gtf.write_text(
        "\n".join(
            [
                'chr1\ttest\ttranscript\t101\t300\t.\t+\t.\tgene_id "g1"; transcript_id "t1";',
                'chr1\ttest\texon\t101\t150\t.\t+\t.\tgene_id "g1"; transcript_id "t1";',
                'chr1\ttest\texon\t251\t300\t.\t+\t.\tgene_id "g1"; transcript_id "t1";',
            ]
        )
        + "\n"
    )

    count = module.convert_annotation_to_bed12(gtf, bed)

    assert count == 1
    fields = bed.read_text().strip().split("\t")
    assert fields[:6] == ["chr1", "100", "300", "t1", "0", "+"]
    assert fields[9:] == ["2", "50,50", "0,150"]


def test_internal_orientation_classifies_reverse_from_sam_lines(tmp_path):
    module = load_module()
    bed = tmp_path / "genes.bed12"
    bed.write_text("chr1\t100\t500\tt1\t0\t+\t100\t500\t0\t1\t400\t0\n")
    sam_lines = [
        "r1\t83\tchr1\t120\t60\t50M\t=\t220\t150\t*\t*",
        "r1\t163\tchr1\t220\t60\t50M\t=\t120\t-150\t*\t*",
        "r2\t83\tchr1\t140\t60\t50M\t=\t240\t150\t*\t*",
        "r2\t163\tchr1\t240\t60\t50M\t=\t140\t-150\t*\t*",
    ]

    result = module.infer_orientation_from_sam_lines(sam_lines, bed, threshold=0.8)

    assert result["classification"] == "reverse"
    assert result["hisat2_rna_strandness"] == "RF"
    assert result["featurecounts_s"] == "2"
    assert result["informative_alignments"] == 4


def test_simulation_dataset_contains_required_files(tmp_path):
    module = load_module()
    dataset = module.create_simulation_dataset(tmp_path, library="reverse", read_count=4)

    assert dataset["genome"].exists()
    assert dataset["annotation"].exists()
    assert dataset["fastq_dir"].exists()
    assert (dataset["fastq_dir"] / "SIM_reverse_1.fastq.gz").exists()
    assert (dataset["fastq_dir"] / "SIM_reverse_2.fastq.gz").exists()