Refactor test_snp.py file

tests/test_snp.py

@@ -0,0 +1,167 @@
+# import glob
+# import os
+# import shutil
+# import subprocess
+# import pytest
+# from datetime import datetime
+# from cookiecutter.main import cookiecutter
+
+
+# @pytest.fixture(scope="module")
+# def repo_path():
+#     path_file = os.path.abspath(__file__)
+#     path_test = os.path.dirname(path_file)
+#     path_repo = os.path.dirname(path_test)
+#     return path_repo
+
+
+# @pytest.fixture(scope="module")
+# def package_path(repo_path):
+#     return os.path.join(repo_path, "seqnado")
+
+
+# @pytest.fixture(scope="module")
+# def pipeline_path(package_path):
+#     return os.path.join(package_path, "workflow", "snakefile_snp")
+
+
+# @pytest.fixture(scope="module")
+# def test_dir_path(repo_path):
+#     return os.path.join(repo_path, "tests")
+
+
+# @pytest.fixture(scope="module")
+# def data_path(test_dir_path):
+#     return os.path.join(test_dir_path, "data")
+
+
+# @pytest.fixture(scope="module")
+# def genome_path(data_path):
+#     return os.path.join(data_path, "genome")
+
+
+# @pytest.fixture(scope="module")
+# def chromsizes(genome_path):
+#     return os.path.join(genome_path, "chr21_rename.fa.fai")
+
+
+# @pytest.fixture(scope="module")
+# def fastqs(data_path):
+#     path = os.path.join(data_path, "fastq")
+#     return glob.glob(os.path.join(path, "snp*.fastq.gz"))
+
+
+# @pytest.fixture(scope="module")
+# def config_path(data_path):
+#     return os.path.join(data_path, "config")
+
+
+# @pytest.fixture(scope="module")
+# def genome_indicies(genome_path):
+#     indicies = os.path.join(genome_path, "bt2")
+
+#     if not os.path.exists(indicies):
+#         try:
+#             import requests
+#             import tarfile
+
+#             url = (
+#                 "https://userweb.molbiol.ox.ac.uk/public/asmith/ngs_pipeline/bt2.tar.gz"
+#             )
+#             output = os.path.join(genome_path, "bt2.tar.gz")
+#             r = requests.get(url, stream=True)
+#             with open(output, "wb") as f:
+#                 f.write(r.content)
+
+#             tar = tarfile.open(output)
+#             tar.extractall(path=genome_path)
+#             tar.close()
+#             os.remove(output)
+#             os.rename(genome_path + "/bt2", indicies)
+
+#         except Exception as e:
+#             print(e)
+#             print("Could not download indicies so generating them")
+#             os.mkdir(indicies)
+#             cmd = f"bowtie2-build {os.path.join(genome_path,'chr21_rename.fa')} {indicies}/bt2 --threads 8"
+#             subprocess.run(cmd.split())
+
+#     return os.path.join(indicies, "chr21")
+
+
+# @pytest.fixture(scope="module")
+# def run_directory(tmpdir_factory):
+#     fn = tmpdir_factory.mktemp("data")
+#     return fn
+
+
+# @pytest.fixture(scope="module", autouse=True)
+# def set_up(
+#     run_directory,
+#     data_path,
+#     package_path,
+#     repo_path,
+#     genome_indicies,
+#     chromsizes,
+#     fastqs,
+#     config_path,
+# ):
+#     cwd = os.getcwd()
+#     os.chdir(run_directory)
+
+#     cookiecutter(
+#         f"{package_path}/workflow/config/cookiecutter_config/config_snp/",
+#         extra_context={
+#             "genome": "hg19",
+#             "date": "{% now 'utc', '%Y-%m-%d' %}",
+#             "project_name": "test",
+#             "chromosome_sizes": chromsizes,
+#             "indicies": genome_indicies,
+#             "design": "design.csv",
+#             "read_type": "paired",
+#             "split_fastq": "True",
+#             "split_fastq_parts": "3",
+#             "remove_pcr_duplicates_method": "picard",
+#             "remove_blacklist": "yes",
+#             "blacklist": f"{data_path}/genome/hg19-blacklist.v2.chr21.bed.gz",
+#             "fasta": f"{data_path}/genome/chr21_rename.fa",
+#             "fasta_index": f"{data_path}/genome/chr21_rename.fa.fai",
+#             "call_snps": "yes",
+#             "annotate_snps": "no",
+#             "make_ucsc_hub": "no",
+#             "UCSC_hub_directory": "test_hub",
+#             "email": "test",
+#             "color_by": "samplename",
+#         },
+#         no_input=True,
+#     )
+
+#     # Move config files and fastq files
+#     current_date = datetime.now().strftime("%Y-%m-%d")
+#     os.chdir(f"{current_date}_test")
+#     for fq in fastqs:
+#         shutil.copy(fq, ".")
+
+#     yield
+
+#     os.chdir(cwd)
+
+
+# def test_pipeline_singularity(genome_path):
+#     indicies_dir = os.path.join(genome_path, "bt2")
+
+#     cmd = [
+#         "seqnado",
+#         "snp",
+#         "--cores",
+#         "4",
+#         "--configfile",
+#         "config_snp.yml",
+#         "--use-singularity",
+#         "--singularity-args",
+#         f'" -B {indicies_dir} -B {genome_path}"',
+#     ]
+#     completed = subprocess.run(" ".join(cmd), shell=True)
+#     assert completed.returncode == 0
+#     assert not os.path.exists("seqnado_error.log")
+#     assert os.path.exists("seqnado_output/")