<commit_before>"""
Tests for snpeff_util.py
"""

"""
Tests for alignment_pipeline.py
"""

import os

from django.test import TestCase
from django.test.utils import override_settings
import vcf
from collections import defaultdict
import re
import itertools

from main.models import AlignmentGroup
from main.models import clean_filesystem_location
from main.models import Dataset
from main.models import ExperimentSample
from main.models import ExperimentSampleToAlignment
from main.models import get_dataset_with_type
from main.models import Project
from main.models import User
from main.models import Variant
from pipeline.variant_effects import build_snpeff
from pipeline.variant_effects import run_snpeff
from pipeline.variant_effects import get_snpeff_config_path
from pipeline.variant_effects import populate_record_eff
from pipeline.snv_calling import call_snvs
from pipeline.snv_calling import VCF_DATASET_TYPE<commit_msg>Get rid of extraneous import. Now passes all tests.<commit_after>"""
Tests for snpeff_util.py
"""

"""
Tests for alignment_pipeline.py
"""

import os

from django.test import TestCase
from django.test.utils import override_settings
import vcf
from collections import defaultdict
import re
import itertools

from main.models import AlignmentGroup
from main.models import clean_filesystem_location
from main.models import Dataset
from main.models import ExperimentSample
from main.models import ExperimentSampleToAlignment
from main.models import get_dataset_with_type
from main.models import Project
from main.models import User
from main.models import Variant
from pipeline.variant_effects import build_snpeff
from pipeline.variant_effects import run_snpeff
from pipeline.variant_effects import get_snpeff_config_path
from pipeline.variant_effects import populate_record_eff
from pipeline.snv_calling import VCF_DATASET_TYPE
{'fraction_non_alphanumeric': 0.03831624392876417, 'fraction_numerical': 0.0, 'mean_word_length': 6.991379310344827, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '251745', 'n_tokens_mistral': 501, 'n_tokens_neox': 492, 'n_words': 177}