def test_import_contigs_valid_input():
expected_output = {"GCA-000007265-protein1_1":"ATGGTACAATATAACAATAATTATCCACAAGACAATAAGGAAGAAGCTATGACGGAAAACGAACAACTATTTTGGAATAGAGTACTAGAGCTATCTCGTTCTCAAATAGCACCAGCAGCTTATGAATTTTTTGTTCTAGAGGCTAGACTCCTCAAAATTGAACATCAAACTGCAGTTATTACTTTAGATAACATTGAAATGAAAAAGCTATTCTGGGAACAAAATTTGGGGCCTGTTATCCTAACAGCTGGTTTTGAAATTTTCAATGCTGAAATTACAGCTAACTATGTCTCAAACGATTTACATTTACAAGAAACTAGTTTTTCTAACTACCAGCAATCTAGCAATGAAGTAAATACTTTACCAATTAGAAAAATCGACTCTAACCTTAAAGAGAAATATACTTTTGCTAATTTTGTTCAAGGAGATGAAAATAGATGGGCTGTTTCAGCATCAATTGCTGTAGCTGATAGTCCTGGCACGACTTATAATCCTCTATTTATCTGGGGGGGACCTGGTCTAGGAAAGACGCATCTACTAAATGCTATTGGAAATCAAGTCTTAAGAGATAATCCAAACGCGAGGGTTTTATACATCACTGCTGAGAATTTTATTAATGAATTTGTCAGTCATATTCGTTTAGATTCGATGGAAGAATTAAAAGAAAAGTTTCGCAACTTAGACTTACTCCTGATTGATGATATTCAGTCGCTTGCTAAGAAAACCTTAGGGGGGACCCAAGAGGAGTTCTTCAATACTTTCAATGCTTTACATACAAACGATAAACAAATCGTATTGACCAGTGACCGAAATCCAAATCAATTAAATGATCTAGAAGAACGTCTAGTCACGCGCTTTAGTTGGGGACTCCCAGTAAATATCACACCACCTGATTTTGAAACACGAGTTGCTATTTTAACCAATAAAATTCAAGAATATCCTTATGATTTTCCTCAAGATACCATTGAATACTTAGCAGGAGAATTTGATTCCAACGTACGTGAATTAGAAGGAGCCTTGAAAAATATTAGTCTAGTTGCTGACTTTAAGCATGCTAAAACTATTACAGTAGATATAGCTGCAGAAGCTATCAGAGCACGTAAAAATGATGGTCCTATTGTTACTGTCATTCCTATAGAAGAAATTCAAATACAAGTTGGTAAATTCTATGGCGTAACTGTAAAAGAGATAAAAGCAACTAAAAGAACACAAGATATTGTCCTTGCAAGACAGGTAGCCATGTACTTAGCTCGTGAGATGACAGATAACAGTCTCCCAAAAATAGGTAAAGAATTTGGGGGACGAGATCACTCAACTGTTCTCCACGCTTATAATAAAATAAAAAATATGGTTGCTCAAGATGACAACTTACGAATTGAGATAGAAACTATCAAAAATAAAATCAGATAG"}
output = rfm.import_contigs("GCA-000007265-protein1.fasta")
assert output == expected_output
def test_import_contigs_invalid_file_inputs(file_input, expected):
"""Tests the behaviour of the import_contigs function with unexpected file inputs"""
assert rfm.import_contigs(file_input) == expected
def test_import_contigs_invalid_inputs(test_input, expectation):
"""Tests the behaviour of the import_contigs function with unexpected inputs"""
with expectation:
rfm.import_contigs(test_input)
(pytest.param("invalid.fasta", {'ContigID': 'REALLIYINAVLIDFASTASEQUENCE'}, marks=pytest.mark.xfail)), # Test with an invalid fasta file input. The file has an ID and an invalid DNA/protein sequence.
(pytest.param("empty.fasta", {'ContigID': ''}, marks=pytest.mark.xfail)), # Test with an empty fasta file input. The file has an ID but no sequence.
("/home/pcerqueira/Lab_Software/testing/tests/GCA-000007265-protein1.fasta", expected_output) # Test with a valid input.
])
def test_import_contigs_invalid_file_inputs(file_input, expected):
"""Tests the behaviour of the import_contigs function with unexpected file inputs"""
assert rfm.import_contigs(file_input) == expected
##############################################################
#### TEST extract_coding_sequences ########################################
orf_file_path = "GCA_000007265.1_ASM726v1_genomic.fna_ORF.txt"
contigs = rfm.import_contigs("GCA_000007265.1_ASM726v1_genomic.fna")
valid_output = rfm.extract_coding_sequences(orf_file_path, contigs, 0, 0)
@pytest.mark.parametrize(
"reading_frames, contigs, starting_id, genome_id, expectation",
[([],[],[],[], pytest.raises(TypeError)), # Test empty list input
("","","","", pytest.raises(FileNotFoundError)), # Test empty string input
# (7,7,7,5, pytest.raises(TypeError)),
(orf_file_path, "", "", "", pytest.raises(TypeError)), # Test with vaild file and empty string input
(orf_file_path, contigs, "", "", pytest.raises(TypeError)), # Test with valid file, contig dict and empty string input
])
def test_extract_coding_sequences_invalid_inputs(reading_frames, contigs, starting_id, genome_id, expectation):
"""Tests the behaviour of the extract_coding_sequences function with unexpected inputs"""
with expectation:
rfm.extract_coding_sequences(reading_frames, contigs, starting_id, genome_id)
def test_import_contigs_existing_empty_txt_input():
rfm.import_contigs("existing.txt")
def test_import_contigs_unexisting_txt_input():
with pytest.raises(FileNotFoundError):
rfm.import_contigs("unexisting.txt")
def test_import_contigs_int_input():
with pytest.raises(TypeError):
rfm.import_contigs(9)
def test_import_contigs_empty_list_input(): rfm.import_contigs([])
def test_import_contigs_no_args():
with pytest.raises(TypeError):
rfm.import_contigs()
