CI
17f8fccf2a
Build pipeline: viash-hub.htrnaseq.fix-create-report-build-hgl2d
Source commit: af02c4b8d7
Source message: Update CHANGELOG
102 lines
4.0 KiB
Python
102 lines
4.0 KiB
Python
import pytest
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import sys
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import pandas as pd
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from pathlib import Path
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from uuid import uuid4
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from shutil import copyfile
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### VIASH START
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meta = {
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"resources_dir": "./src/eset/create_fdata/",
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"executable": "target/executable/eset/create_fdata/create_fdata",
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"config": "src/eset/create_fdata/config.vsh.yaml"
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}
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### VIASH END
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@pytest.fixture
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def test_annotation_path():
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return Path(meta["resources_dir"]) / "test_annotation.gtf"
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@pytest.fixture
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def random_path(tmp_path):
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def wrapper(extension=None):
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extension = "" if not extension else f".{extension}"
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return tmp_path / f"{uuid4()}{extension}"
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return wrapper
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def test_create_fdata(run_component, test_annotation_path, random_path):
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output_path = random_path("tsv")
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run_component([
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"--gtf", test_annotation_path,
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"--output", output_path
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])
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assert output_path.is_file()
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result = pd.read_csv(output_path, sep="\t", dtype=pd.StringDtype())
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expected_dict = {
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"seqname": ["20", "20", "20", "21"],
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"start": ["87250", "142590", "157454", "297570"],
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"end": ["97094", "145751", "159163", "300321"],
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"strand": ["+", "+", "+", "+"],
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"gene_id": ["ENSG00000178591", "ENSG00000125788",
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"ENSG00000088782", "ENSG00000247315"],
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"gene_version": ["7", "6", "5", "4"],
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"gene_name": ["DEFB125", "DEFB126", "DEFB127", pd.NA],
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"gene_source": ["ensembl_havana", "ensembl_havana",
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"ensembl_havana", "havana"],
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"gene_biotype": ["protein_coding", "protein_coding",
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"protein_coding", "protein_coding"],
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"ENSEMBL_with_version": ["ENSG00000178591.7", "ENSG00000125788",
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"ENSG00000088782", "ENSG00000247315"],
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"ENSEMBL": ["ENSG00000178591", "ENSG00000125788",
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"ENSG00000088782", "ENSG00000247315"],
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"SYMBOL": ["DEFB125", "DEFB126", "DEFB127", pd.NA]
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}
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expected = pd.DataFrame.from_dict(expected_dict, dtype=pd.StringDtype())
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pd.testing.assert_frame_equal(expected, result, check_like=True)
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def test_make_unique(run_component, test_annotation_path, random_path):
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gtf_with_duplicate_entry_path = random_path("gtf")
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output_path = random_path("tsv")
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entry_to_add = (
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"\n20 ensembl_havana gene 87250 97094 . + . gene_id " +
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"\"ENSG00000178591.7\"; gene_version \"7\"; gene_name \"DEFB125\"; " +
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"gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\";\n"
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)
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copyfile(test_annotation_path, gtf_with_duplicate_entry_path)
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with gtf_with_duplicate_entry_path.open("a") as open_gtf:
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open_gtf.write(entry_to_add)
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run_component([
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"--gtf", gtf_with_duplicate_entry_path,
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"--output", output_path
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])
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assert output_path.is_file()
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result = pd.read_csv(output_path, sep="\t", dtype=pd.StringDtype())
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expected_dict = {
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"seqname": ["20", "20", "20", "21"],
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"start": ["87250", "142590", "157454", "297570"],
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"end": ["97094", "145751", "159163", "300321"],
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"strand": ["+", "+", "+", "+"],
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"gene_id": ["ENSG00000178591", "ENSG00000125788",
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"ENSG00000088782", "ENSG00000247315"],
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"gene_version": ["7", "6", "5", "4"],
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"gene_name": ["DEFB125", "DEFB126", "DEFB127", pd.NA],
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"gene_source": ["ensembl_havana", "ensembl_havana",
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"ensembl_havana", "havana"],
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"gene_biotype": ["protein_coding", "protein_coding",
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"protein_coding", "protein_coding"],
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"ENSEMBL_with_version": ["ENSG00000178591.7", "ENSG00000125788",
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"ENSG00000088782", "ENSG00000247315"],
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"ENSEMBL": ["ENSG00000178591", "ENSG00000125788",
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"ENSG00000088782", "ENSG00000247315"],
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"SYMBOL": ["DEFB125", "DEFB126", "DEFB127", pd.NA]
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}
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expected = pd.DataFrame.from_dict(expected_dict, dtype=pd.StringDtype())
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pd.testing.assert_frame_equal(expected, result, check_like=True)
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if __name__ == '__main__':
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sys.exit(pytest.main([__file__])) |