def test_run(self):
"""test run"""
sorted_bam = os.path.join(data_dir, "run.bam")
ref_fasta = os.path.join(data_dir, "run.ref.fa")
outprefix = "tmp.het_snp_caller.run"
hsc = het_snp_caller.HetSnpCaller(sorted_bam, ref_fasta, outprefix)
hsc.run()
expected_per_contig = os.path.join(data_dir,
"run.expect.per_contig.tsv")
expected_summary = os.path.join(data_dir, "run.expect.summary.tsv")
got_per_contig = outprefix + ".per_contig.tsv"
got_summary = outprefix + ".summary.tsv"
got_vcf = outprefix + ".het_calls.vcf"
self.assertTrue(
filecmp.cmp(expected_per_contig, got_per_contig, shallow=False))
self.assertTrue(
filecmp.cmp(expected_summary, got_summary, shallow=False))
expected_lines = [
"ref1\t251\t.\tC\tA,<*>\t0\t.\tDP=31;ADF=9,5,0;ADR=9,7,0;AD=18,12,0;I16=9,9,5,7,716,28496,479,19121,900,45000,528,23232,279,5591,203,4283;QS=0.599163,0.400837,0;VDB=0.670984;SGB=-0.680642;RPB=0.596826;MQB=2.89016e-05;MQSB=0.932405;BQB=0.994415;MQ0F=0\tPL\t251,0,255,255,255,255\n"
]
with open(got_vcf) as f:
got_lines = [x for x in f if not x.startswith("#")]
self.assertEqual(expected_lines, got_lines)
os.unlink(got_per_contig)
os.unlink(got_summary)
os.unlink(got_vcf)
def test_run(self):
"""test run"""
sorted_bam = os.path.join(data_dir, "run.bam")
ref_fasta = os.path.join(data_dir, "run.ref.fa")
outprefix = "tmp.het_snp_caller.run"
hsc = het_snp_caller.HetSnpCaller(sorted_bam, ref_fasta, outprefix)
hsc.run()
expected_per_contig = os.path.join(data_dir,
"run.expect.per_contig.tsv")
expected_summary = os.path.join(data_dir, "run.expect.summary.tsv")
got_per_contig = outprefix + ".per_contig.tsv"
got_summary = outprefix + ".summary.tsv"
got_vcf = outprefix + ".het_calls.vcf"
self.assertTrue(
filecmp.cmp(expected_per_contig, got_per_contig, shallow=False))
self.assertTrue(
filecmp.cmp(expected_summary, got_summary, shallow=False))
expected_lines = [
"ref1\t251\t.\tC\tA,<*>\t0\t.\tDP=31;ADF=9,5,0;ADR=9,8,0;AD=18,13,0;I16=9,9,5,8,720,28800,520,20800,900,45000,572,25168,279,5591,203,4283;QS=0.580645,0.419355,0;VDB=0.78464;SGB=-0.683931;RPBZ=0.621123;MQBZ=-5.47723;MQSBZ=-0.626654;BQBZ=0;SCBZ=0;FS=0;MQ0F=0\tPL\t255,0,255,255,255,255\n"
]
with open(got_vcf) as f:
got_lines = [x for x in f if not x.startswith("#")]
self.assertEqual(expected_lines, got_lines)
os.unlink(got_per_contig)
os.unlink(got_summary)
os.unlink(got_vcf)
def run(self):
try:
os.mkdir(self.outdir)
except:
raise Exception("Error making output directory " + self.outdir)
outprefix = os.path.join(self.outdir, "samtools_qc")
samfile = os.path.join(self.outdir, "tmp.sam")
SamtoolsQc._map_reads(self.ref_fasta, self.reads1, self.reads2,
samfile)
SamtoolsQc._make_stats_and_plots(samfile, self.ref_fasta, outprefix)
hsc = het_snp_caller.HetSnpCaller(
samfile, self.ref_fasta, os.path.join(self.outdir, "het_snps"))
hsc.run()
self.stats = SamtoolsQc.stats_from_report(outprefix + ".stats")
os.unlink(samfile)
def run(self):
try:
os.mkdir(self.outdir)
except:
raise Error('Error making output directory ' + self.outdir)
outprefix = os.path.join(self.outdir, 'samtools_qc')
samfile = os.path.join(self.outdir, 'tmp.sam')
SamtoolsQc._map_reads(self.ref_fasta, self.reads1, self.reads2,
samfile)
SamtoolsQc._make_stats_and_plots(samfile, self.ref_fasta, outprefix)
hsc = het_snp_caller.HetSnpCaller(
samfile, self.ref_fasta, os.path.join(self.outdir, 'het_snps'))
hsc.run()
self.stats = SamtoolsQc.stats_from_report(outprefix + '.stats')
os.unlink(samfile)