def test_snpeff():
# a custom refrence
fh_log = TempFile()
mydata = snpeff.SnpEff(reference=sequana_data("JB409847.gbk"), log=fh_log.name)
with TempFile() as fh:
mydata.launch_snpeff(sequana_data("JB409847.vcf"), fh.name)
fh_log.delete()
# cleanup
try:
os.remove("snpEff.config")
except:
pass
try:
os.remove("snpEff_genes.txt")
except:
pass
try:
os.remove("snpEff_summary.html")
except:
pass
try:
snpeff.SnpEff(reference="dummy")
assert False
except SystemExit:
assert True
except:
assert False
def test_add_locus_with_modification():
# Alter the original GBK to alter the locus name
data = open(sequana_data("JB409847.gbk"), "r").read()
newdata = data.replace("JB409847", "DUMMY_JB409847")
fh = TempFile(suffix="gbk")
with open(fh.name, 'w') as fout:
fout.write(newdata)
# Now we read this new GBK file that has a different locus name as
# compared to the fasta
mydata = snpeff.SnpEff(reference=fh.name)
# Here is the corresponding FASTA
fasta = sequana_data("JB409847.fasta")
with TempFile(suffix="fasta") as fh2:
mydata.add_locus_in_fasta(fasta, fh2.name)
# In theory, in the newly created fasta file, we should find back the
# DUMMY tag
# cleanup
try:
os.remove("snpEff.config")
except:
pass
data = open(fh2.name, "r").read()
assert "DUMMY" in data
fh.delete()
def test_add_locus_no_modification():
mydata = snpeff.SnpEff(reference=sequana_data("JB409847.gbk"))
with TempFile() as fh:
fastafile = sequana_data("JB409847.fasta")
mydata.add_locus_in_fasta(fastafile, fh.name)
# cleanup
try:
os.remove("snpEff.config")
except:
pass