<commit_before>"""Test individual components of the analysis pipeline.
"""
import os
import shutil
import unittest

from nose.plugins.attrib import attr

from bcbio.distributed.messaging import parallel_runner
from bcbio.pipeline.config_utils import load_config
from bcbio.pipeline import run_info
from bcbio.provenance import programs
from bcbio.variation import vcfutils

class RunInfoTest(unittest.TestCase):
    def setUp(self):
        self.data_dir = os.path.join(os.path.dirname(__file__), "data")

    @attr(speed=1)
    def test_programs(self):
        """Identify programs and versions used in analysis.
        """
        config = load_config(os.path.join(self.data_dir, "automated",
                                          "post_process-sample.yaml"))
        print programs.get_versions(config)

class VCFUtilTest(unittest.TestCase):
    """Test various utilities for dealing with VCF files.
    """
    def setUp(self):
        self.data_dir = os.path.join(os.path.dirname(__file__), "data")<commit_msg>Fix bug in test_pipeline.py relating to change in programs._get_versions() name<commit_after>"""Test individual components of the analysis pipeline.
"""
import os
import shutil
import unittest

from nose.plugins.attrib import attr

from bcbio.distributed.messaging import parallel_runner
from bcbio.pipeline.config_utils import load_config
from bcbio.pipeline import run_info
from bcbio.provenance import programs
from bcbio.variation import vcfutils

class RunInfoTest(unittest.TestCase):
    def setUp(self):
        self.data_dir = os.path.join(os.path.dirname(__file__), "data")

    @attr(speed=1)
    def test_programs(self):
        """Identify programs and versions used in analysis.
        """
        config = load_config(os.path.join(self.data_dir, "automated",
                                          "post_process-sample.yaml"))
        print programs._get_versions(config)

class VCFUtilTest(unittest.TestCase):
    """Test various utilities for dealing with VCF files.
    """
    def setUp(self):
        self.data_dir = os.path.join(os.path.dirname(__file__), "data")
{'fraction_non_alphanumeric': 0.09587090650213574, 'fraction_numerical': 0.0009492168960607499, 'mean_word_length': 3.4851063829787234, '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': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5073658', 'n_tokens_mistral': 613, 'n_tokens_neox': 609, 'n_words': 158}