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"""
Test sanity of various output formats for a minimal real-world example.
"""
import csv
import os.path
import re
import subprocess
import tempfile
import pytest
os.environ["PACBIO_TEST_ENV"] = "1" # turns off --verbose
DATA_DIR = "/pbi/dept/secondary/siv/testdata/kineticsTools"
REF_DIR = "/pbi/dept/secondary/siv/references/Helicobacter_pylori_J99"
ALIGNMENTS = os.path.join(DATA_DIR, "Hpyl_1_5000.xml")
REFERENCE = os.path.join(REF_DIR, "sequence", "Helicobacter_pylori_J99.fasta")
@pytest.mark.internal_data
class TestOutputs:
@classmethod
def setup_class(cls):
# prefix = tempfile.NamedTemporaryFile().name # not sure of the
# problem, but misused anyway
prefix = 'TestOutputs'
cls.csv_file = "{p}.csv".format(p=prefix)
cls.gff_file = "{p}.gff".format(p=prefix)
cls.bw_file = "{p}.bw".format(p=prefix)
args = [
"ipdSummary", "--log-level", "WARNING",
"--csv", cls.csv_file,
"--gff", cls.gff_file,
#"--bigwig", cls.bw_file,
"--numWorkers", "12",
"--pvalue", "0.001",
"--identify", "m6A,m4C",
"--referenceStride", "100",
"--referenceWindows", "gi|12057207|gb|AE001439.1|:0-200",
"--reference", REFERENCE,
"--useChemistry", "P6-C4", # FIXME hacky workaround
ALIGNMENTS
]
print(" ".join(args))
assert subprocess.call(args) == 0
with open(cls.csv_file) as f:
cls.csv_records = [l.split(",") for l in f.read().splitlines()][1:]
@classmethod
def teardown_class(cls):
return
for fn in [cls.csv_file, cls.gff_file, cls.bw_file]:
if os.path.exists(fn):
os.remove(fn)
def test_csv_output(self):
assert len(self.csv_records) == 400
assert self.csv_records[0][3] == "A"
assert self.csv_records[100][3] == "T"
@pytest.mark.skip(reason="missing bw_file, so i disabled this (cd)")
def test_bigwig(self):
import pyBigWig
f = pyBigWig.open(self.bw_file)
for i_rec, rec in enumerate(self.csv_records):
seqid = re.sub('\"', "", rec[0])
tpl = int(rec[1]) - 1
s = int(f.values(seqid, tpl, tpl + 1)[0])
ipd_minus = (s % 65536) / 100.0
ipd_plus = (s >> 16) / 100.0
if rec[2] == "1":
assert pytest.approx(ipd_minus, float(rec[8]))
else:
assert pytest.approx(ipd_plus, float(rec[8]))
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