def test__validate_library_id_valid(self):
input_dicts_list = [{
ns_test._get_library_name_key(): "CV4",
ns_test._get_library_fp_key(): "/some/path/to/CV4.txt",
ns_test._get_library_settings_keys()[0]: "19",
ns_test._get_library_settings_keys()[1]: "21"
}]
ns_test._validate_library_id("CV4", input_dicts_list)
def test__validate_settings_keys_valid(self):
input_settings = {
ns_test._get_library_name_key(): "CV4",
ns_test._get_library_fp_key(): "/some/path/to/CV4.txt",
ns_test._get_library_settings_keys()[0]: "19",
ns_test._get_library_settings_keys()[1]: "21"
}
ns_test._validate_settings_keys("CV4", input_settings)
def test__id_and_validate_library_missing_values(self):
input_dicts_list = [{
ns_test._get_library_name_key(): "CV4",
ns_test._get_library_fp_key(): "/some/path/to/CV4.txt",
ns_test._get_library_settings_keys()[0]: "",
ns_test._get_library_settings_keys()[1]: "21"
}]
with self.assertRaises(ValueError):
ns_test._id_and_validate_library("CV4", input_dicts_list)
def test__id_and_validate_library_valid(self):
expected_output = {
ns_test._get_library_name_key(): "CV4",
ns_test._get_library_fp_key(): "/some/path/to/CV4.txt",
ns_test._get_library_settings_keys()[0]: "19",
ns_test._get_library_settings_keys()[1]: "21"
}
input_dicts_list = [expected_output]
real_output = ns_test._id_and_validate_library("CV4", input_dicts_list)
self.assertEqual(expected_output, real_output)
def test__validate_settings_keys_error(self):
expected_settings = {
ns_test._get_library_name_key(): "CV4",
ns_test._get_library_fp_key(): "/some/path/to/CV4.txt",
ns_test._get_library_settings_keys()[0]: "19",
ns_test._get_library_settings_keys()[1]: "21"
}
input_settings = {
ns_test._get_library_name_key(): "CV4",
ns_test._get_library_fp_key(): "/some/path/to/CV4.txt"
}
with self.assertRaises(ValueError):
ns_test._validate_settings_keys("CV4", input_settings)
def test__validate_library_id_error_too_many(self):
input_dicts_list = [{
ns_test._get_library_name_key(): "CV4",
ns_test._get_library_fp_key(): "/some/path/to/CV4.txt",
ns_test._get_library_settings_keys()[0]: "19",
ns_test._get_library_settings_keys()[1]: "21"
}, {
ns_test._get_library_name_key(): "CV4",
ns_test._get_library_fp_key(): "/old/path/to/CV4.txt",
ns_test._get_library_settings_keys()[0]: "19",
ns_test._get_library_settings_keys()[1]: "21"
}]
with self.assertRaises(ValueError):
ns_test._validate_library_id("CV4", input_dicts_list)
def test__validate_settings_keys_valid_w_warning(self):
input_settings = {
ns_test._get_library_name_key(): "CV4",
ns_test._get_library_fp_key(): "/some/path/to/CV4.txt",
ns_test._get_library_settings_keys()[0]: "19",
ns_test._get_library_settings_keys()[1]: "21",
"key2": "goldish"
}
with warnings.catch_warnings(record=True) as warnings_list:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
ns_test._validate_settings_keys("CV4", input_settings)
assert len(warnings_list) == 1
assert "ignored" in str(warnings_list[-1].message)
def test__validate_settings_keys_error_w_warning(self):
# inputs are missing the expected key "library_name" but have a typo of it instead
input_settings = {
"libraryname": "CV4",
ns_test._get_library_fp_key(): "/some/path/to/CV4.txt",
ns_test._get_library_settings_keys()[0]: "19",
ns_test._get_library_settings_keys()[1]: "21"
}
with warnings.catch_warnings(record=True) as warnings_list:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
with self.assertRaises(ValueError):
ns_test._validate_settings_keys("CV4", input_settings)
assert len(warnings_list) == 1
assert "ignored" in str(warnings_list[-1].message)
def test__id_and_validate_library_too_many_libs(self):
expected_output = {
ns_test._get_library_name_key(): "CV4",
ns_test._get_library_fp_key(): "/some/path/to/CV4.txt",
ns_test._get_library_settings_keys()[0]: "19",
ns_test._get_library_settings_keys()[1]: "21"
}
input_dicts_list = [
expected_output, {
ns_test._get_library_name_key(): "CV4",
ns_test._get_library_fp_key(): "/old/path/to/CV4.txt",
ns_test._get_library_settings_keys()[0]: "19",
ns_test._get_library_settings_keys()[1]: "21"
}
]
with self.assertRaises(ValueError):
ns_test._id_and_validate_library("CV4", input_dicts_list)
def test__mine_library_file_valid(self):
file_contents_str = """# library_name = CV4
# min_trimmed_grna_len = 19
# max_trimmed_grna_len = 21
construct_id target_a_id probe_a_id probe_a_seq target_b_id probe_b_id probe_b_seq FinalSequence Gene_A_chr Gene_A_pos Gene_B_chr Gene_B_pos
BRCA1_chr17_41276018__NonTargetingControlGuideForHuman0412 BRCA1 BRCA1_chr17_41276018 TCTTGTGCTGACTTACCAGA NonTargetingControlGuideForHuman0412 NonTargetingControlGuideForHuman0412 GCACGCTGTACAGACGACAA tatatatcttgtggaaaggacgaaacACCGTCTTGTGCTGACTTACCAGAGTTTcAGAGCTAtgctgGAAActgcaTAGCAAGTTgAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTGTACTGAGtCGCCCaGTCTCAGATAGATCCGACGCCGCCATCTCTAGGCCCGCGCCGGCCCCCTCGCACAGACTTGTGGGAGAAGCTCGGCTACTCCCCTGCCCCGGTTAATTTGCATATAATATTTCCTAGTAACTATAGAGGCTTAATGTGCGATAAAAGAGGCACGCTGTACAGACGACAAGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGG chr17 41276018 NA NA
NonTargetingControlGuideForHuman0352__SETD2_chr3_47142972 NonTargetingControlGuideForHuman0352 NonTargetingControlGuideForHuman0352 GCCATTCTAGTCCCGGCATA SETD2 SETD2_chr3_47142972 AACGTTAACTCTGAGCCTGA tatatatcttgtggaaaggacgaaacACCGGCCATTCTAGTCCCGGCATAGTTTcAGAGCTAtgctgGAAActgcaTAGCAAGTTgAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTGTACTGAGtCGCCCaGTCTCAGATAGATCCGACGCCGCCATCTCTAGGCCCGCGCCGGCCCCCTCGCACAGACTTGTGGGAGAAGCTCGGCTACTCCCCTGCCCCGGTTAATTTGCATATAATATTTCCTAGTAACTATAGAGGCTTAATGTGCGATAAAAGAGAACGTTAACTCTGAGCCTGAGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGG NA NA chr3 47142972
"""
expected_output = {
ns_test._get_library_name_key(): "CV4",
ns_test._get_library_fp_key(): "/some/path/to/CV4.txt",
ns_test._get_library_settings_keys()[1]: "19",
ns_test._get_library_settings_keys()[0]: "21"
}
file_contents_obj = io.StringIO(file_contents_str)
real_output = ns_test._mine_library_file("CV4",
"/some/path/to/CV4.txt",
file_contents_obj)
self.assertEqual(expected_output, real_output)
