diff --git a/test/test_start_stop.py b/test/test_start_stop.py index 5e5eab99..411e53ca 100644 --- a/test/test_start_stop.py +++ b/test/test_start_stop.py @@ -2,24 +2,24 @@ from bakta.features import signal_peptides as bu -oneTwentyone_fwd = {'start': 1, 'stop': 21, 'strand': '+'} -oneTwentyone_rev = {'start': 1, 'stop': 21, 'strand': '-'} -fourFifteen_fwd = {'start': 4, 'stop': 15, 'strand': '+'} -fourFifteen_rev = {'start': 4, 'stop': 15, 'strand': '-'} +one_twentyone_fwd = {'start': 1, 'stop': 21, 'strand': '+'} +one_twentyone_rev = {'start': 1, 'stop': 21, 'strand': '-'} +four_fifteen_fwd = {'start': 4, 'stop': 15, 'strand': '+'} +four_fifteen_rev = {'start': 4, 'stop': 15, 'strand': '-'} @pytest.mark.parametrize( "orf, start, stop, expected", [ # Forward strand - (oneTwentyone_fwd, 1, 3, (1,9)), # ORF spans whole sequence length, signal peptide starts at AA 1 - (oneTwentyone_fwd, 2, 7, (4,21)), # ORF spans whole sequence length, signal peptide stops at last AA - (fourFifteen_fwd, 1, 3, (4,12)), # ORF does not span whole sequence length, signal peptide starts at AA 1 - (fourFifteen_fwd, 2, 4, (7,15)), # ORF does not span whole sequence length, signal peptide stops at last AA + (one_twentyone_fwd, 1, 3, (1,9)), # ORF spans whole sequence length, signal peptide starts at AA 1 + (one_twentyone_fwd, 2, 7, (4,21)), # ORF spans whole sequence length, signal peptide stops at last AA + (four_fifteen_fwd, 1, 3, (4,12)), # ORF does not span whole sequence length, signal peptide starts at AA 1 + (four_fifteen_fwd, 2, 4, (7,15)), # ORF does not span whole sequence length, signal peptide stops at last AA # Reverse strand - (oneTwentyone_rev, 1, 3, (13,21)), # ORF spans whole sequence length, signal peptide starts at AA 1 - (oneTwentyone_rev, 3, 7, (1,15)), # ORF spans whole sequence length, signal peptide stops at last AA - (fourFifteen_rev, 1, 2, (10,15)), # ORF does not span whole sequence length, signal peptide starts at AA 1 - (fourFifteen_rev, 2, 3, (7,12)) # ORF does not span whole sequence length, signal peptide in the middle of ORF + (one_twentyone_rev, 1, 3, (13,21)), # ORF spans whole sequence length, signal peptide starts at AA 1 + (one_twentyone_rev, 3, 7, (1,15)), # ORF spans whole sequence length, signal peptide stops at last AA + (four_fifteen_rev, 1, 2, (10,15)), # ORF does not span whole sequence length, signal peptide starts at AA 1 + (four_fifteen_rev, 2, 3, (7,12)) # ORF does not span whole sequence length, signal peptide in the middle of ORF ] ) def test_start_stop(orf, start, stop, expected):