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test_ncbi_process_mito.py
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import os
import unittest
from unittest.mock import MagicMock, patch
from Bio.SeqRecord import SeqRecord
from sbin.ncbi_process_mito import (
download_mito_files,
get_mito_genes,
parse_db_xrefs,
parse_nomenclature_value,
)
BASE_DIR = os.path.dirname(os.path.abspath(__file__))
class TestNcbiProcessMito(unittest.TestCase):
def verify_mito_gene_attributes(self, mito_gene, expected_values):
for k, v in expected_values.items():
try:
self.assertEqual(getattr(mito_gene, k), v)
except AssertionError:
print(
f"Test failure on mito gene {mito_gene.gene_symbol} ({mito_gene.gene_id}) "
f'attribute "{k}" with value "{v}" not equal to "{getattr(mito_gene, k)}"'
)
raise
@patch("sbin.ncbi_process_mito.download_from_eutils")
def test_download_mito_files(self, mock_download):
output_dir = "test_dir"
accession = "test_accession"
result = download_mito_files(output_dir, accession)
self.assertEqual(
result,
{
"gbff": "test_dir/test_accession.gbff",
"fna": "test_dir/test_accession.fna",
},
)
mock_download.assert_any_call(accession, "gb", f"{output_dir}/{accession}.gbff")
mock_download.assert_any_call(
accession, "fasta", f"{output_dir}/{accession}.fna"
)
def test_db_xrefs(self):
gb_feature_mock = MagicMock(spec=SeqRecord)
gb_feature_mock.qualifiers = {
"db_xref": ["GeneID:4558", "HGNC:HGNC:7481", "MIM:590070"]
}
result = parse_db_xrefs(gb_feature_mock)
self.assertEqual(
result, {"GeneID": "4558", "HGNC": "HGNC:7481", "MIM": "590070"}
)
def test_db_xrefs_empty(self):
gb_feature_mock = MagicMock(spec=SeqRecord)
gb_feature_mock.qualifiers = {}
result = parse_db_xrefs(gb_feature_mock)
self.assertEqual(result, {})
def test_parse_nomenclature_value(self):
gb_feature_mock = MagicMock(spec=SeqRecord)
gb_feature_mock.qualifiers = {
"nomenclature": [
"Official Symbol: MT-TF | Name: mitochondrially encoded tRNA phenylalanine | Provided by: HGNC:HGNC:7481"
]
}
result = parse_nomenclature_value(gb_feature_mock)
self.assertEqual(
result,
{
"Official Symbol": "MT-TF",
"Name": "mitochondrially encoded tRNA phenylalanine",
"Provided by": "HGNC:HGNC:7481",
},
)
def test_parse_nomenclature_value_empty(self):
gb_feature_mock = MagicMock(spec=SeqRecord)
gb_feature_mock.qualifiers = {}
result = parse_nomenclature_value(gb_feature_mock)
self.assertEqual(result, {})
def test_get_mito_genes(self):
mito_genbank_filepath = f"{BASE_DIR}/data/NC_012920.1.gbff"
results = [_ for _ in get_mito_genes(mito_genbank_filepath)]
expected_gene_ids = [
4508,
4509,
4511,
4512,
4513,
4514,
4519,
4535,
4536,
4537,
4538,
4539,
4540,
4541,
4549,
4550,
4553,
4555,
4556,
4558,
4563,
4564,
4565,
4566,
4567,
4568,
4569,
4570,
4571,
4572,
4573,
4574,
4575,
4576,
4577,
4578,
4579,
]
expected_gene_symbols = [
"MT-ATP6",
"MT-ATP8",
"MT-CO1",
"MT-CO2",
"MT-CO3",
"MT-CYB",
"MT-ND1",
"MT-ND2",
"MT-ND3",
"MT-ND4",
"MT-ND4L",
"MT-ND5",
"MT-ND6",
"MT-RNR1",
"MT-RNR2",
"MT-TA",
"MT-TC",
"MT-TD",
"MT-TE",
"MT-TF",
"MT-TG",
"MT-TH",
"MT-TI",
"MT-TK",
"MT-TL1",
"MT-TL2",
"MT-TM",
"MT-TN",
"MT-TP",
"MT-TQ",
"MT-TR",
"MT-TS1",
"MT-TS2",
"MT-TT",
"MT-TV",
"MT-TW",
"MT-TY",
]
expected_origin = "NCBI"
expected_aln_method = "splign"
self.assertEqual(len(results), 37)
self.assertEqual(sorted([r.gene_id for r in results]), expected_gene_ids)
self.assertEqual(
sorted([r.gene_symbol for r in results]), expected_gene_symbols
)
self.assertEqual([r.origin for r in results], [expected_origin] * 37)
self.assertEqual(
[r.alignment_method for r in results], [expected_aln_method] * 37
)
results_by_gene = {mg.gene_id: mg for mg in results}
# Expected results for "MT-TV" non-coding tRNA gene on the plus strand
expected_mg4577_values = {
"gene_symbol": "MT-TV",
"name": "mitochondrially encoded tRNA valine",
"tx_ac": "NC_012920.1_01601_01670",
"tx_seq": "CAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGA",
"tx_start": 0,
"tx_end": 69,
"alt_ac": "NC_012920.1",
"alt_start": 1601,
"alt_end": 1670,
"strand": 1,
"transl_table": None,
"transl_except": None,
"pro_ac": None,
"pro_seq": None,
}
self.verify_mito_gene_attributes(results_by_gene[4577], expected_mg4577_values)
# Expected results for "MT-TQ" tRNA gene on the minus strand
expected_mg4572_values = {
"gene_symbol": "MT-TQ",
"name": "mitochondrially encoded tRNA glutamine",
"tx_ac": "NC_012920.1_04328_04400",
"tx_seq": "TAGGATGGGGTGTGATAGGTGGCACGGAGAATTTTGGATTCTCAGGGATGGGTTCGATTCTCATAGTCCTAG",
"tx_start": 0,
"tx_end": 72,
"alt_ac": "NC_012920.1",
"alt_start": 4328,
"alt_end": 4400,
"strand": -1,
"transl_table": None,
"transl_except": None,
"pro_ac": None,
"pro_seq": None,
}
self.verify_mito_gene_attributes(results_by_gene[4572], expected_mg4572_values)
# Expected results for "MT-CO2" coding gene on the plus strand
expected_mg4513_values = {
"gene_symbol": "MT-CO2",
"name": "mitochondrially encoded cytochrome c oxidase II",
"tx_ac": "NC_012920.1_07585_08269",
"tx_seq": "ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTT"
"TCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACT"
"ATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGG"
"CCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCC"
"TTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTA"
"AAAACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAG"
"TTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACCCTATAG",
"tx_start": 0,
"tx_end": 684,
"alt_ac": "NC_012920.1",
"alt_start": 7585,
"alt_end": 8269,
"strand": 1,
"transl_table": "2",
"transl_except": None,
"pro_ac": "YP_003024029.1",
"pro_seq": "MAHAAQVGLQDATSPIMEELITFHDHALMIIFLICFLVLYALFLTLTTKLTNTNISDAQEMETVWTILPAIILVLIALPSLRILYMTDEVNDP"
"SLTIKSIGHQWYWTYEYTDYGGLIFNSYMLPPLFLEPGDLRLLDVDNRVVLPIEAPIRMMITSQDVLHSWAVPTLGLKTDAIPGRLNQTTFTATRPGVYYGQCS"
"EICGANHSFMPIVLELIPLKIFEMGPVFTL",
}
self.verify_mito_gene_attributes(results_by_gene[4513], expected_mg4513_values)
# Expected results for "MT-ND1" coding gene on the minus strand with a transl_except
expected_mg4535_values = {
"gene_symbol": "MT-ND1",
"name": "mitochondrially encoded NADH dehydrogenase 1",
"tx_ac": "NC_012920.1_03306_04262",
"tx_seq": "ATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATAC"
"AACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCACATCT"
"ACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGG"
"CCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAG"
"TAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAA"
"CACCTCTGATTACTCCTGCCATCATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTC"
"CGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCACCACTA"
"CAATCTTCCTAGGAACAACATATGACGCACTCTCCCCTGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGA"
"ACAGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTAGCATTACTTATATGATATGTCTCCATACCCAT"
"TACAATCTCCAGCATTCCCCCTCAAACCTA",
"tx_start": 0,
"tx_end": 956,
"alt_ac": "NC_012920.1",
"alt_start": 3306,
"alt_end": 4262,
"strand": 1,
"transl_table": "2",
"transl_except": ["(pos:4261..4262,aa:TERM)"],
"pro_ac": "YP_003024026.1",
"pro_seq": "MPMANLLLLIVPILIAMAFLMLTERKILGYMQLRKGPNVVGPYGLLQPFADAMKLFTKEPLKPATSTITLYITAPTLALTIALLLWTPLPMPN"
"PLVNLNLGLLFILATSSLAVYSILWSGWASNSNYALIGALRAVAQTISYEVTLAIILLSTLLMSGSFNLSTLITTQEHLWLLLPSWPLAMMWFISTLAETNRTP"
"FDLAEGESELVSGFNIEYAAGPFALFFMAEYTNIIMMNTLTTTIFLGTTYDALSPELYTTYFVTKTLLLTSLFLWIRTAYPRFRYDQLMHLLWKNFLPLTLALL"
"MWYVSMPITISSIPPQT",
}
self.verify_mito_gene_attributes(results_by_gene[4535], expected_mg4535_values)