class PeptideMassValidatorTestCase(unittest.TestCase):
"""
Tests peptide mass validator with modified peptides.
"""
PRECURSOR = mass_to_int(1751.868942379)
"""Precursor
"""
PRECURSOR_RANGE = PrecursorRange(PRECURSOR, 5, 5)
"""Precursor tolerance
"""
PEPTIDE_SEQUENCES = [
("VYMGWJKGVYTTYR", "VYM[v:any:15994915000]GWJKGVYTTYR"),
("AVMQCVTVQSKPYNK", "AVMQC[s:any:57021464000]VTVQSKPYNK"),
("MTEYPDVJWGTRIR", "M[v:any:15994915000]TEYPDVJWGTRIR"),
("EPEHJDVJMPRMAAK", "EPEHJDVJMPRM[v:any:15994915000]AAK"),
("WYMAZLVWJIZER", "WYM[v:any:15994915000]AZLVWJIZER"),
("CGCJVHJJMFFJAR",
"C[s:any:57021464000]GC[s:any:57021464000]JVHJJM[v:any:15994915000]FFJAR"
), ("CVPPPQSATDJQNVAR", "C[s:any:57021464000]VPPPQSATDJQNVAR"),
("LJPYRVPFTPMCDK",
"LJPYRVPFTPM[v:any:15994915000]C[s:any:57021464000]DK"),
("VFFTWESJTVHCVK", "VFFTWESJTVHC[s:any:57021464000]VK"),
("JSYNCDIEJRASRR", "JSYNC[s:any:57021464000]DIEJRASRR"),
("QYECRRVOWYR", "QYEC[s:any:57021464000]RRVOWYR"),
("AYYWJNRGFYJMR", "AYYWJNRGFYJMR"),
("JQATYMTSGGTSPPITK", "JQATYMTSGGTSPPITK"),
("ODGANVQZRTBPMAJ", "ODGANVQZRTBPMAJ"),
("QJMVFGKQQCQLEK",
"QJM[v:any:15994915000]VFGKQQC[s:any:57021464000]QLEK"),
("PAPVHCDYPPYPVJK", "PAPVHC[s:any:57021464000]DYPPYPVJK"),
("VBLVVTBMDHVHMVK", "VBLVVTBMDHVHM[v:any:15994915000]VK"),
("MIHCPAFYRIMAVK",
"MIHC[s:any:57021464000]PAFYRIM[v:any:15994915000]AVK"),
("QMYFARHJHDGLHK", "QMYFARHJHDGLHK"),
("QJDJRMBTTFDBKR", "QJDJRMBTTFDBKR"),
("QRTEFCREIGEVTK", "QRTEFC[s:any:57021464000]REIGEVTK"),
("HKDDRTVQLFAMYL", "HKDDRTVQLFAM[v:any:15994915000]YL"),
("VAEPMFDRVMRMVR", "VAEPMFDRVM[v:any:15994915000]RMVR"),
("WTEQAPSJYJMGGRK", "WTEQAPSJYJM[v:any:15994915000]GGRK"),
("ATVFPQLKEQJVTUK", "ATVFPQLKEQJVTUK"),
("FQSVVBFVEBIHYR", "FQSVVBFVEBIHYR"),
("ZVVCCJVJSABIYGR",
"ZVVC[s:any:57021464000]C[s:any:57021464000]JVJSABIYGR"),
("EGRSAAAETCVVFSLR", "EGRSAAAETC[s:any:57021464000]VVFSLR"),
("HQQMDAVTKSPGTQPK", "HQQMDAVTKSPGTQPK"),
("VDFAFVQRPKCEEK", "VDFAFVQRPKC[s:any:57021464000]EEK"),
("DQMCPFRJCKJIR",
"DQM[v:any:15994915000]C[s:any:57021464000]PFRJC[s:any:57021464000]KJIR"
),
("MCMHTJRIVEFKR",
"M[v:any:15994915000]C[s:any:57021464000]M[v:any:15994915000]HTJRIVEFKR"
), ("JJSPGDYTPHVTHGMK", "JJSPGDYTPHVTHGMK"),
("FVKMYGRFJCYPR",
"FVKM[v:any:15994915000]YGRFJC[s:any:57021464000]YPR"),
("CIMPYRGRTIQWR",
"C[s:any:57021464000]IM[v:any:15994915000]PYRGRTIQWR"),
("FYVDVHMFTJQQPK", "FYVDVHMFTJQQPK"),
("ODBRVBFMYAAIGK", "ODBRVBFM[v:any:15994915000]YAAIGK"),
("FFVMCRPNDRVVGR", "FFVMC[s:any:57021464000]RPNDRVVGR"),
("UPMVTQPAGPPIIPKR", "UPMVTQPAGPPIIPKR"),
("FTBDTIVVTNZFPQK", "FTBDTIVVTNZFPQK"),
("JMQWKCFVPJVCR",
"JM[v:any:15994915000]QWKC[s:any:57021464000]FVPJVC[s:any:57021464000]R"
), ("YKQFTFFMGJAEVR", "YKQFTFFM[v:any:15994915000]GJAEVR"),
("HTVVJTFJJSKUVSTG", "HTVVJTFJJSKUVSTG"),
("WAKQJSNRCTFWR", "WAKQJSNRC[s:any:57021464000]TFWR"),
("JSJGWZBJCWAYJK", "JSJGWZBJC[s:any:57021464000]WAYJK"),
("YYSNIHNQAIVRQF", "YYSNIHNQAIVRQF"),
("REVJRDIMFPMGEK",
"REVJRDIM[v:any:15994915000]FPM[v:any:15994915000]GEK"),
("MJNCMTWAGKQKLR",
"MJNC[s:any:57021464000]M[v:any:15994915000]TWAGKQKLR"),
("FGILPJSVRWQUTGK", "FGILPJSVRWQUTGK"),
("YYPGKPEPMKRENK", "YYPGKPEPM[v:any:15994915000]KRENK"),
("JTMVDENNWAJKYR", "JTMVDENNWAJKYR"),
("QQYMICAJAPMVRR",
"QQYMIC[s:any:57021464000]AJAPM[v:any:15994915000]VRR"),
("CIGFEQKIKBZQMK", "C[s:any:57021464000]IGFEQKIKBZQMK"),
("FQAIBSPMVKTMBVR", "FQAIBSPMVKTM[v:any:15994915000]BVR"),
("LIDFIZAZLAVTIUR", "LIDFIZAZLAVTIUR"),
("YAMKPASAMJKMJGPAG", "YAMKPASAM[v:any:15994915000]JKMJGPAG"),
("PQNGPZQPJZTCKQK", "PQNGPZQPJZTC[s:any:57021464000]KQK"),
("MCIQMQJKYPPRR",
"M[v:any:15994915000]C[s:any:57021464000]IQM[v:any:15994915000]QJKYPPRR"
), ("CWNHPAKJVWWQK", "C[s:any:57021464000]WNHPAKJVWWQK"),
("WZGQTAVGZAQQOGR", "WZGQTAVGZAQQOGR"),
("MQCDJGHSORKQR", "MQC[s:any:57021464000]DJGHSORKQR"),
("TSFFHFVINNKDQR", "TSFFHFVINNKDQR"),
("WLQQJAGTEQPYYR", "WLQQJAGTEQPYYR"),
("TCMTDDRIRPVJJY", "TC[s:any:57021464000]MTDDRIRPVJJY"),
("MKGBMIPSJAZVYQR", "MKGBM[v:any:15994915000]IPSJAZVYQR"),
("KGAHJQQQDADAAPFR", "KGAHJQQQDADAAPFR"),
("EVWVGYTDGRJVCAK", "EVWVGYTDGRJVC[s:any:57021464000]AK"),
("OAYIJRPUFRSNK", "OAYIJRPUFRSNK"),
("BCDAVMAVBAJPIVHK", "BC[s:any:57021464000]DAVMAVBAJPIVHK"),
("QJPMCKFPYEPAKK",
"QJPM[v:any:15994915000]C[s:any:57021464000]KFPYEPAKK"),
("UHRFRQVFJFPVR", "UHRFRQVFJFPVR"),
("QMPJOAASZWBPQK", "QM[v:any:15994915000]PJOAASZWBPQK"),
("CMGJEJLDVKKMDGK",
"C[s:any:57021464000]M[v:any:15994915000]GJEJLDVKKMDGK"),
("VDCDJTQJJEQKYK", "VDC[s:any:57021464000]DJTQJJEQKYK"),
("NVVNFDVPVMVJMEF", "NVVNFDVPVMVJMEF"),
("MJVQVCFIJNDTQR",
"M[v:any:15994915000]JVQVC[s:any:57021464000]FIJNDTQR"),
("DVJACKGQSRTQGJGY", "DVJAC[s:any:57021464000]KGQSRTQGJGY"),
("JQCPJQCRYVKCK",
"JQC[s:any:57021464000]PJQC[s:any:57021464000]RYVKC[s:any:57021464000]K"
), ("MNPASVJEMTJFJMR", "MNPASVJEMTJFJMR"),
("IPDTQRYKMAJCEK", "IPDTQRYKMAJC[s:any:57021464000]EK"),
("HAOSJPJVUGKMPAK", "HAOSJPJVUGKM[v:any:15994915000]PAK"),
("VSTPVRJFMVACGCR",
"VSTPVRJFMVAC[s:any:57021464000]GC[s:any:57021464000]R"),
("CVGGAKALDYHYJSAK", "C[s:any:57021464000]VGGAKALDYHYJSAK"),
("RVVEPFAYCJEDVR", "RVVEPFAYC[s:any:57021464000]JEDVR"),
("CJMPMMVPMKVQKK",
"C[s:any:57021464000]JMPM[v:any:15994915000]M[v:any:15994915000]VPMKVQKK"
), ("ZQRYJFVYMTFZK", "ZQRYJFVYMTFZK"),
("JGTWPASJHDSLYHR", "JGTWPASJHDSLYHR"),
("HTBDTEZJCROIK", "HTBDTEZJC[s:any:57021464000]ROIK"),
("ALWJEYSRCJEANK", "ALWJEYSRC[s:any:57021464000]JEANK"),
("WGDSCDIGAJJPPVPR", "WGDSC[s:any:57021464000]DIGAJJPPVPR"),
("MJREDFJIEIWCK", "MJREDFJIEIWC[s:any:57021464000]K"),
("VGHQMAMGPPJVDQJK",
"VGHQM[v:any:15994915000]AM[v:any:15994915000]GPPJVDQJK"),
("WGAYRRJYWYYR", "WGAYRRJYWYYR"),
("KGQRVYZMNBQTJR", "KGQRVYZM[v:any:15994915000]NBQTJR"),
("SWMQEKSPVFWAIK", "SWM[v:any:15994915000]QEKSPVFWAIK"),
("FKQAGTVMYMYJJR",
"FKQAGTVM[v:any:15994915000]YM[v:any:15994915000]YJJR"),
("BJPVSFPQBHGTWVR", "BJPVSFPQBHGTWVR"),
("QDGLJJPFWNMYQK", "QDGLJJPFWNMYQK"),
("DCITAMHPAKPMPKR", "DC[s:any:57021464000]ITAMHPAKPMPKR"),
("BMJZMJVDYJPRMK", "BMJZMJVDYJPRMK")
]
"""Plain and PTM annotated peptide seqeunces
"""
MODIFICATION_COLLECTION: ClassVar[
ModificationCollection] = ModificationCollection.read_from_csv_file(
pathlib.Path("./test_files/modifications.csv"))
"""Modification Collection
"""
NUMBER_OF_VARIABLE_MODIFICATIONS: ClassVar[int] = 3
"""Number of variable modifications
"""
def test_validation(self):
"""
Checks if mass validation works.
"""
peptide_mass_validator = PeptideMassValidator(
self.__class__.MODIFICATION_COLLECTION,
self.__class__.NUMBER_OF_VARIABLE_MODIFICATIONS,
self.__class__.PRECURSOR_RANGE)
for plain_sequence, annotated_sequence in self.__class__.PEPTIDE_SEQUENCES:
peptide = Peptide(plain_sequence,
Trypsin.count_missed_cleavages(plain_sequence))
self.assertTrue(
peptide_mass_validator.validate(peptide, True),
f"expected: {annotated_sequence}; is: {peptide.sequence_with_modification_markers}"
)
def test_with_real_data(self):
VARIABLE_MODIFICATION_LIMIT = 2
# Mass of MFPVTJEDTEGNVJTVSPPCYGFJQJR
PRECURSOR = 3025492916648
PRECURSOR_TOLERANCE = 20
# With the given mass, tolerance and modifications 3 peptides shoud be found
modifications_file_path = pathlib.Path(
'./test_files/modifications.csv')
work_dir = pathlib.Path(f"./tmp/{self.id()}")
test_files_path = pathlib.Path('./test_files')
protein_data_test_file_path = test_files_path.joinpath('proteins.txt')
self.prepare_workdir(work_dir, test_files_path,
protein_data_test_file_path)
maintenance = DatabaseMaintenance(os.getenv("TEST_MACPEPDB_URL"),
work_dir, 4, 5, 'Trypsin', 2, 5, 40)
maintenance.start()
modification_collection = ModificationCollection.read_from_csv_file(
modifications_file_path)
peptide_mass_validator = PeptideMassValidator(
modification_collection, VARIABLE_MODIFICATION_LIMIT,
PrecursorRange(PRECURSOR, PRECURSOR_TOLERANCE,
PRECURSOR_TOLERANCE))
validated_matching_peptide_sequences = set()
with self.database_connection:
with self.database_connection.cursor() as database_cursor:
# Run through all peptides (in batches of 1000 peptides) and check which matchs the precursor and modification requirements
database_cursor.execute(
f"SELECT sequence, number_of_missed_cleavages FROM {Peptide.TABLE_NAME};"
)
while True:
rows = database_cursor.fetchmany(1000)
if not len(rows):
break
for row in rows:
peptide = Peptide(row[0], row[1])
if peptide_mass_validator.validate(peptide):
validated_matching_peptide_sequences.add(
peptide.sequence)
with self.database_connection:
with self.database_connection.cursor() as database_cursor:
modification_combination_list = ModificationCombinationList(
modification_collection, PRECURSOR, PRECURSOR_TOLERANCE,
PRECURSOR_TOLERANCE, VARIABLE_MODIFICATION_LIMIT)
where_conditions = modification_combination_list.to_where_condition(
)
peptides = Peptide.select(database_cursor,
where_conditions,
fetchall=True)
queried_matching_peptide_sequences = set()
for peptide in peptides:
queried_matching_peptide_sequences.add(peptide.sequence)
# Check length of both manually validated set and the queried set
self.assertEqual(len(validated_matching_peptide_sequences),
len(queried_matching_peptide_sequences))
# Cross check if peptide from one set is in the other set
for sequence in queried_matching_peptide_sequences:
self.assertIn(sequence,
validated_matching_peptide_sequences)
for sequence in validated_matching_peptide_sequences:
self.assertIn(sequence, queried_matching_peptide_sequences)