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test_generate_fasta.py
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test_generate_fasta.py
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import unittest
import os
import sys
import tempfile
from subprocess import call
from filecmp import cmp
import py_compile
from pvacseq.lib import generate_fasta
import pvacseq
class GenerateFastaTests(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/' + 'generate_fasta.py'
cls.test_data_dir = os.path.join(base_dir, 'tests', 'test_data', 'generate_fasta')
cls.peptide_sequence_length = '21'
cls.epitope_length = '8'
def test_source_compiles(self):
self.assertTrue(py_compile.compile(self.executable))
def test_input_file_with_peptide_sequence_length_17_generates_expected_file(self):
peptide_sequence_length = '17'
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_peptide_sequence_length_17.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_peptide_sequence_length_17.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_peptide_sequence_length_21_generates_expected_file(self):
peptide_sequence_length = '21'
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_peptide_sequence_length_21.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_peptide_sequence_length_21.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_peptide_sequence_length_31_generates_expected_file(self):
peptide_sequence_length = '31'
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_peptide_sequence_length_31.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_peptide_sequence_length_31.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_mutation_at_relative_end_of_full_sequence_generates_expected_file(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_mutation_at_relative_end_of_full_sequence.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_mutation_at_relative_end_of_full_sequence.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_mutation_at_relative_end_of_full_sequence.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_mutation_at_relative_beginning_of_full_sequence_generates_expected_file(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_mutation_at_relative_beginning_of_full_sequence.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_mutation_at_relative_beginning_of_full_sequence.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_mutation_at_relative_beginning_of_full_sequence.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_wildtype_sequence_shorter_than_desired_peptide_sequence_length_generates_expected_file(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_short_wildtype_sequence.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_short_wildtype_sequence.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_short_wildtype_sequence.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_multiple_transcripts_generates_expected_file(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_multiple_transcripts.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_multiple_transcripts.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_multiple_transcripts.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_multiple_transcripts_per_alternate_allele_generates_expected_file(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_multiple_transcripts_per_alt.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_multiple_transcripts_per_alt.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_multiple_transcripts_per_alt.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_position_out_of_bounds_generates_empty_output_file(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_position_out_of_bounds.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
self.assertEqual(os.stat(generate_fasta_output_file.name).st_size, 0)
self.assertEqual(os.stat(generate_fasta_key_output_file.name).st_size, 0)
def test_input_file_with_inframe_insertion_amino_acid_replacement_generates_expected_file(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_inframe_insertion_aa_replacement.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_inframe_insertion_aa_replacement.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_inframe_insertion_aa_replacement.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_inframe_deletion_amino_acid_replacement_generates_expected_file(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_inframe_deletion_aa_replacement.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_inframe_deletion_aa_replacement.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_inframe_deletion_aa_replacement.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_inframe_insertion_amino_acid_insertion_generates_expected_file(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_inframe_insertion_aa_insertion.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_inframe_insertion_aa_insertion.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_inframe_insertion_aa_insertion.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_inframe_deletion_amino_acid_deletion_generates_expected_file(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_inframe_deletion_aa_deletion.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_inframe_deletion_aa_deletion.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_inframe_deletion_aa_deletion.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_inframe_deletion_range(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_inframe_deletion_range.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_inframe_deletion_range.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_inframe_deletion_range.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_frameshift_variant_feature_truncation_generates_expected_file(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_frameshift_variant_feature_truncation.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_frameshift_variant_feature_truncation.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_frameshift_variant_feature_truncation.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_frameshift_variant_feature_elongation_generates_expected_file(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_frameshift_variant_feature_elongation.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_frameshift_variant_feature_elongation.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_frameshift_variant_feature_elongation.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_frameshift_variant_range_generates_expected_file(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_frameshift_variant_range.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_frameshift_variant_range.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_frameshift_variant_range.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_sequence_containing_asterisk(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_asterisk_sequence.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_asterisk_sequence.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_asterisk_sequence.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_sequence_containing_X(self):
peptide_sequence_length = '31'
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_X_sequence.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_X_sequence.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_X_sequence.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_input_file_with_resulting_short_fasta_sequence(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_short_fasta_sequence.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python,
self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_short_fasta_sequence.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_short_fasta_sequence.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_downstream_sequence_length_limit_generates_expected_file(self):
generate_fasta_input_file = os.path.join(self.test_data_dir, 'input_frameshift_variant_feature_elongation.tsv')
generate_fasta_output_file = tempfile.NamedTemporaryFile()
generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
self.assertFalse(call([
self.python, self.executable,
generate_fasta_input_file,
self.peptide_sequence_length,
self.epitope_length,
generate_fasta_output_file.name,
generate_fasta_key_output_file.name,
'-d', '20'
], shell=False))
expected_output_file = os.path.join(self.test_data_dir, 'output_downstream_sequence_length_limit.fasta')
self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
expected_key_output_file = os.path.join(self.test_data_dir, 'output_downstream_sequence_length_limit.key')
self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
def test_distance_from_start_works_as_expected(self):
sequence = 'KKLKILGMPFRNIRSILKMVN'
position = 5
self.assertEqual(generate_fasta.distance_from_start(position, sequence), 5)
def test_distance_from_end_works_as_expected(self):
sequence = 'KKLKILGMPFRNIRSILKMVN'
position = 5
self.assertEqual(generate_fasta.distance_from_end(position, sequence), 15)
if __name__ == '__main__':
unittest.main()