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test_convert_vcf.py
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test_convert_vcf.py
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import unittest
import os
import sys
import tempfile
from subprocess import call
from filecmp import cmp
import py_compile
import pvacseq
class ConvertVcfTests(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.python = sys.executable
base_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file__)), '..'))
cls.executable = os.path.dirname(pvacseq.__file__) + '/lib/' + 'convert_vcf.py'
cls.test_data_dir = os.path.join(base_dir, 'tests', 'test_data', 'convert_vcf')
def test_source_compiles(self):
self.assertTrue(py_compile.compile(self.executable))
def test_input_vcf_generates_expected_tsv(self):
convert_vcf_input_file = os.path.join(self.test_data_dir, 'input.vcf')
convert_vcf_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python, self.executable, convert_vcf_input_file, convert_vcf_output_file.name
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output.tsv')
self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))
def test_input_vcf_with_cufflinks_files_generates_expected_tsv(self):
convert_vcf_input_file = os.path.join(self.test_data_dir, 'full_input.vcf')
convert_vcf_output_file = tempfile.NamedTemporaryFile()
convert_vcf_cufflinks_genes_file = os.path.join(self.test_data_dir, 'genes.fpkm_tracking')
convert_vcf_cufflinks_isoforms_file = os.path.join(self.test_data_dir, 'isoforms.fpkm_tracking')
self.assertFalse(call([
self.python,
self.executable,
convert_vcf_input_file,
convert_vcf_output_file.name,
'--gene-expn-file', convert_vcf_cufflinks_genes_file,
'--transcript-expn-file', convert_vcf_cufflinks_isoforms_file,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_cufflinks.tsv')
self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))
def test_input_vcf_with_bam_readcount_files_generates_expected_tsv(self):
convert_vcf_input_file = os.path.join(self.test_data_dir, 'full_input.vcf')
convert_vcf_output_file = tempfile.NamedTemporaryFile()
convert_vcf_normal_snvs_file = os.path.join(self.test_data_dir, 'snvs.bam_readcount')
convert_vcf_normal_indels_file = os.path.join(self.test_data_dir, 'indels.bam_readcount')
self.assertFalse(call([
self.python,
self.executable,
convert_vcf_input_file,
convert_vcf_output_file.name,
'--tdna-snvs-coverage-file', convert_vcf_normal_snvs_file,
'--tdna-indels-coverage-file', convert_vcf_normal_indels_file,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_bam_readcount.tsv')
self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))
def test_input_vcf_with_multiple_transcripts_generates_expected_tsv(self):
convert_vcf_input_file = os.path.join(self.test_data_dir, 'input_multiple_transcripts.vcf')
convert_vcf_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python, self.executable, convert_vcf_input_file, convert_vcf_output_file.name
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_multiple_transcripts.tsv')
self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))
def test_input_vcf_with_multiple_transcripts_per_alt_generates_expected_tsv(self):
convert_vcf_input_file = os.path.join(self.test_data_dir, 'input_multiple_transcripts_per_alt.vcf')
convert_vcf_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python, self.executable, convert_vcf_input_file, convert_vcf_output_file.name
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_multiple_transcripts_per_alt.tsv')
self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))
def test_input_vcf_with_mutation_at_relative_beginning_of_full_sequence_generates_expected_tsv(self):
convert_vcf_input_file = os.path.join(self.test_data_dir, 'input_mutation_at_relative_beginning_of_full_sequence.vcf')
convert_vcf_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python, self.executable, convert_vcf_input_file, convert_vcf_output_file.name
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_mutation_at_relative_beginning_of_full_sequence.tsv')
self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))
def test_input_vcf_with_mutation_at_relative_end_of_full_sequence_generates_expected_tsv(self):
convert_vcf_input_file = os.path.join(self.test_data_dir, 'input_mutation_at_relative_end_of_full_sequence.vcf')
convert_vcf_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python, self.executable, convert_vcf_input_file, convert_vcf_output_file.name
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_mutation_at_relative_end_of_full_sequence.tsv')
self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))
def test_input_vcf_with_position_out_of_bounds_generates_expected_tsv(self):
convert_vcf_input_file = os.path.join(self.test_data_dir, 'input_position_out_of_bounds.vcf')
convert_vcf_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python, self.executable, convert_vcf_input_file, convert_vcf_output_file.name
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_position_out_of_bounds.tsv')
self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))
def test_input_vcf_with_short_wildtype_sequence_generates_expected_tsv(self):
convert_vcf_input_file = os.path.join(self.test_data_dir, 'input_short_wildtype_sequence.vcf')
convert_vcf_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python, self.executable, convert_vcf_input_file, convert_vcf_output_file.name
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_short_wildtype_sequence.tsv')
self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))
def test_input_vcf_with_frameshift_variant_feature_elongation_generates_expected_tsv(self):
convert_vcf_input_file = os.path.join(self.test_data_dir, 'input_frameshift_variant_feature_elongation.vcf')
convert_vcf_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python, self.executable, convert_vcf_input_file, convert_vcf_output_file.name
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_frameshift_variant_feature_elongation.tsv')
self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))
def test_input_vcf_with_frameshift_variant_feature_truncation_generates_expected_tsv(self):
convert_vcf_input_file = os.path.join(self.test_data_dir, 'input_frameshift_variant_feature_truncation.vcf')
convert_vcf_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python, self.executable, convert_vcf_input_file, convert_vcf_output_file.name
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_frameshift_variant_feature_truncation.tsv')
self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))
def test_input_vcf_with_inframe_insertion_amino_acid_replacement_generates_expected_tsv(self):
convert_vcf_input_file = os.path.join(self.test_data_dir, 'input_inframe_insertion_aa_replacement.vcf')
convert_vcf_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python, self.executable, convert_vcf_input_file, convert_vcf_output_file.name
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_inframe_insertion_aa_replacement.tsv')
self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))
def test_input_vcf_with_inframe_deletion_amino_acid_replacement_generates_expected_tsv(self):
convert_vcf_input_file = os.path.join(self.test_data_dir, 'input_inframe_deletion_aa_replacement.vcf')
convert_vcf_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python, self.executable, convert_vcf_input_file, convert_vcf_output_file.name
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_inframe_deletion_aa_replacement.tsv')
self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))
def test_input_vcf_with_inframe_insertion_amino_acid_insertion_generates_expected_tsv(self):
convert_vcf_input_file = os.path.join(self.test_data_dir, 'input_inframe_insertion_aa_insertion.vcf')
convert_vcf_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python, self.executable, convert_vcf_input_file, convert_vcf_output_file.name
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_inframe_insertion_aa_insertion.tsv')
self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))
def test_input_vcf_with_inframe_deletion_amino_acid_deletion_expected_tsv(self):
convert_vcf_input_file = os.path.join(self.test_data_dir, 'input_inframe_deletion_aa_deletion.vcf')
convert_vcf_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python, self.executable, convert_vcf_input_file, convert_vcf_output_file.name
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_inframe_deletion_aa_deletion.tsv')
self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))