def test_chr12(self, config):
config["snpcheck"]["used"] = ["common", "all", 0.001]
db = PrimerDB(config['database'], dump=config['ampliconbed'])
name_to_dump = "DNM1L"
results = zippy.zippyPrimerQuery(config,
"12:32895523-32895682",
True,
None,
db,
None, [0],
name_to_dump=name_to_dump,
noncoding=False,
combine=True,
getgenes=None)
assert len(results[0]) == 0, results
config["snpcheck"]["used"] = ["common", "all", 0.08]
db = PrimerDB(config['database'], dump=config['ampliconbed'])
results = zippy.zippyPrimerQuery(config,
"12:32895523-32895682",
True,
None,
db,
None, [0],
name_to_dump=name_to_dump,
noncoding=False,
combine=True,
getgenes=None)
assert len(results[0]) > 0, results
def test_base0_vs_base1(self, config):
db = PrimerDB(config['database'], dump=config['ampliconbed'])
zippy.gplist = None
name_to_dump = "DNM1L"
config["exon_numbering_base"] = 0
results0 = zippy.zippyPrimerQuery(config,
"12:32895523-32895682",
True,
None,
db,
None, [0],
name_to_dump=name_to_dump,
noncoding=False,
combine=True,
getgenes=None)
zippy.gplist = None
config["exon_numbering_base"] = 1
results1 = zippy.zippyPrimerQuery(config,
"12:32895523-32895682",
True,
None,
db,
None, [0],
name_to_dump=name_to_dump,
noncoding=False,
combine=True,
getgenes=None)
logger.info("ress0 {}".format(results0))
logger.info("ress1 {}".format(results1))
zippy.gplist = None
def test_chr6(self, config):
config["snpcheck"]["used"] = ["common", "all", 0.000001]
db = PrimerDB(config['database'], dump=config['ampliconbed'])
results = zippy.zippyPrimerQuery(config,
"6:26092913-26093188",
True,
None,
db,
None, [0],
name_to_dump=None)
exon_number = 1 + config["exon_numbering_base"]
logger.debug(f"ress {results}")
assert len(results[0]) == 0, results
config["snpcheck"]["used"] = ["common", "all", 0.007]
db = PrimerDB(config['database'], dump=config['ampliconbed'])
results = zippy.zippyPrimerQuery(config,
"6:26092913-26093188",
True,
None,
db,
None, [0],
name_to_dump=None)
exon_number = 1 + config["exon_numbering_base"]
logger.debug(f"ress {results}")
assert len(results[0]) > 0, results
def test_chrX(self, config):
config["snpcheck"]["used"] = ["common", "all", 0.1]
db = PrimerDB(config['database'], dump=config['ampliconbed'])
name_to_dump = "RBM10"
results = zippy.zippyPrimerQuery(config,
"X:47045555-47045786",
True,
None,
db,
None, [
0,
],
name_to_dump=name_to_dump,
noncoding=False,
combine=True,
getgenes=None)
assert len(results[0]) > 0, results
config["snpcheck"]["used"] = ["common", "all"]
db = PrimerDB(config['database'], dump=config['ampliconbed'])
name_to_dump = "RBM10"
results = zippy.zippyPrimerQuery(config,
"X:47045555-47045786",
True,
None,
db,
None, [
0,
],
name_to_dump=name_to_dump,
noncoding=False,
combine=True,
getgenes=None)
assert len(results[0]) > 0, results
def test_chr22(self, config):
config["snpcheck"]["used"] = ["common", "all", 0.000001]
db = PrimerDB(config['database'], dump=config['ampliconbed'])
name_to_dump = "HFE"
results = zippy.zippyPrimerQuery(config,
"22:41568503-41568667",
True,
None,
db,
None, [0],
name_to_dump=name_to_dump,
noncoding=False,
combine=True,
getgenes=None)
assert len(results[0]) == 0, results
config["snpcheck"]["used"] = ["common", "all", 0.1]
db = PrimerDB(config['database'], dump=config['ampliconbed'])
name_to_dump = "HFE"
results = zippy.zippyPrimerQuery(config,
"22:41568503-41568667",
True,
None,
db,
None, [0],
name_to_dump=name_to_dump,
noncoding=False,
combine=True,
getgenes=None)
assert len(results[0]) > 0, results
def test_primerexonname6(self, config):
db = PrimerDB(config['database'], dump=config['ampliconbed'])
zippy.gplist = None
results = zippy.zippyPrimerQuery(config,
"6:26091069-26091332",
True,
None,
db,
None, [0, 1, 2],
name_to_dump=None)
assert 0, results
def test_primerexonname3(self, config):
db = PrimerDB(config['database'], dump=config['ampliconbed'])
zippy.gplist = None
results = zippy.zippyPrimerQuery(config,
"12:32895351-32895785",
True,
None,
db,
None, [0, 1, 2],
name_to_dump="DNM1L")
assert 0, results
def test_chr12_2missing(self, config):
db = PrimerDB(config['database'], dump=config['ampliconbed'])
zippy.gplist = None
results = zippy.zippyPrimerQuery(config,
"12:115115461-115116484",
True,
None,
db,
None, [0, 1, 2],
name_to_dump=None)
assert len(results[0]) == 0, results
def test_primerexonname2(self, config):
db = PrimerDB(config['database'], dump=config['ampliconbed'])
name_to_dump = "DNM1L"
results = zippy.zippyPrimerQuery(config,
"12:32895523-32895682",
True,
None,
db,
None, [0],
name_to_dump=name_to_dump,
noncoding=False,
combine=True,
getgenes=None)
def test_chr11(self, config):
db = PrimerDB(config['database'], dump=config['ampliconbed'])
zippy.gplist = None
results = zippy.zippyPrimerQuery(config,
"11:118343121-118343321",
True,
None,
db,
None, [0, 1, 2],
name_to_dump=None)
logging.info(f"chr11 {results}")
exon_number = 2 + config["exon_numbering_base"]
assert results[0][0][0:2] == ['11:118343121-118343321', f'KMT2A_{exon_number}_2-3'],\
results
def test_primerexonname208(self, config):
db = PrimerDB(config['database'], dump=config['ampliconbed'])
zippy.gplist = None
results = zippy.zippyPrimerQuery(config,
"12:25398208-25398318",
True,
None,
db,
None, [0, 1, 2],
name_to_dump="KRAS")
exon_number = 1 + config["exon_numbering_base"]
assert results[0][0][0:2] == [
'12:25398208-25398318', f'KRAS_{exon_number}'
], results
def test_snplimits(self, config):
db = PrimerDB(config['database'], dump=config['ampliconbed'])
zippy.gplist = None
config["designlimits"]["criticalsnp"] == 20
config["designlimits"]["snpcount"] == 20
results = zippy.zippyPrimerQuery(config,
"uploads/NEB_S2.smCounter.anno.vcf",
True,
None,
db,
None, [0, 1, 2],
name_to_dump=None)
zippy.gplist = None
config["designlimits"]["criticalsnp"] == 0
config["designlimits"]["snpcount"] == 0
results2 = zippy.zippyPrimerQuery(config,
"uploads/NEB_S2.smCounter.anno.vcf",
True,
None,
db,
None, [0, 1, 2],
name_to_dump=None)
zippy.gplist = None
assert results == results2, (results, results2)
#!/usr/bin/env python
import unittest, pysam, json, sys
from zippy import zippy
from zippy.zippylib import range_string
from zippy.zippylib.database import PrimerDB
with open("zippy/zippy.json") as conf:
config = json.load(conf)
db = PrimerDB(config['database'],dump=config['ampliconbed'])
zippy.gplist = None
results = zippy.zippyPrimerQuery(config, sys.argv[1], True, None, db,
None, [0, 1, 2], name_to_dump=sys.argv[2])