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import os.path as op
import tempfile
from collections import defaultdict
import pytest
from pbcommand.testkit import PbIntegrationBase
DATA_DIR = "/pbi/dept/secondary/siv/testdata/kineticsTools"
REF_DIR = "/pbi/dept/secondary/siv/references"
EXPECTED_GFF = """\
Escherichia_coli_K12\tkinModCall\tmodified_base\t6307\t6307\t34\t-\t.\tcoverage=56;context=CAGATTAGCACGCTGATGCGCATCAGCGACAAACTGGCGGG;IPDRatio=1.92
Escherichia_coli_K12\tkinModCall\tmodified_base\t6455\t6455\t32\t-\t.\tcoverage=53;context=CCTGCAAGGACTGGATATGCTGATTCTTATTTCACCTGCGA;IPDRatio=1.78
Escherichia_coli_K12\tkinModCall\tmodified_base\t6512\t6512\t32\t-\t.\tcoverage=55;context=GTAATCACAACTATCGATCAACTCATTCTCATTTTTTGCTA;IPDRatio=1.81
Escherichia_coli_K12\tkinModCall\tm6A\t6984\t6984\t34\t-\t.\tcoverage=56;context=TACTGGCGGGTAACGGCACAACCTACATGCCGCTGGAAGGT;IPDRatio=2.02;frac=0.627;fracLow=0.321;fracUp=0.911;identificationQv=5
Escherichia_coli_K12\tkinModCall\tm4C\t7111\t7111\t24\t+\t.\tcoverage=19;context=GGAGGCCAGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGA;IPDRatio=2.45;frac=1.000;fracLow=0.370;fracUp=1.000;identificationQv=4
Escherichia_coli_K12\tkinModCall\tmodified_base\t20051\t20051\t44\t+\t.\tcoverage=19;context=ACGTCAAAGGGTGACAGCAGGCTCATAAGACGCCCCAGCGT;IPDRatio=2.54
Escherichia_coli_K12\tkinModCall\tm4C\t20296\t20296\t24\t-\t.\tcoverage=17;context=GGATGCCGGGCAACAGCCCGCATTATGGGCGTTGGCCTCAA;IPDRatio=1.86;frac=1.000;fracLow=0.379;fracUp=1.000;identificationQv=9
Escherichia_coli_K12\tkinModCall\tmodified_base\t20449\t20449\t31\t+\t.\tcoverage=18;context=TGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGT;IPDRatio=2.49"""
class TestKineticsTools(PbIntegrationBase):
def test_help(self):
args = ["ipdSummary", "--help"]
self._check_call(args)
@pytest.mark.internal_data
def test_ecoli_first_50k(self):
gff_out = tempfile.NamedTemporaryFile(suffix=".gff").name
csv_out = tempfile.NamedTemporaryFile(suffix=".csv").name
ref_set = op.join(REF_DIR, "ecoli_k12_MG1655_first50k",
"ecoli_k12_MG1655_first50k.referenceset.xml")
alignments = op.join(DATA_DIR, "ecoli_first_50k.mapped.bam")
args = [
"ipdSummary",
"--gff", gff_out,
"--csv", csv_out,
"--pvalue", "0.001",
"--identify", "m6A,m4C",
"--methylFraction",
"--reference", ref_set,
alignments
]
self._check_call(args)
assert op.isfile(gff_out)
assert op.isfile(csv_out)
records = []
print(gff_out)
with open(gff_out, "rt") as gff:
for line in gff.read().splitlines():
if not line.startswith("##"):
records.append(line)
for rec1, rec2 in zip(records, EXPECTED_GFF.splitlines()):
assert rec1 == rec2
csv_records = []
with open(csv_out, "rt") as csv:
for line in csv.read().splitlines():
csv_records.append(line)
assert len(csv_records) == 3222
assert csv_records[1] == \
r'"Escherichia_coli_K12",6214,0,C,8,0.784,0.144,0.631,1.242,33,,,'
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