def _get_total_alignment_score(self, gene_name):
tmp_bam = os.path.join(self.root_dir,
'tmp.get_total_alignment_score.bam')
assert not os.path.exists(tmp_bam)
tmp_fa = os.path.join(self.root_dir,
'tmp.get_total_alignment_score.ref.fa')
assert not os.path.exists(tmp_fa)
faidx.write_fa_subset([gene_name],
self.genes_fa,
tmp_fa,
samtools_exe=self.samtools_exe,
verbose=self.verbose)
mapping.run_bowtie2(
self.reads1,
self.reads2,
tmp_fa,
tmp_bam[:-4],
threads=self.threads,
samtools=self.samtools_exe,
bowtie2=self.bowtie2_exe,
bowtie2_preset=self.bowtie2_preset,
verbose=self.verbose,
)
score = mapping.get_total_alignment_score(tmp_bam)
os.unlink(tmp_bam)
os.unlink(tmp_fa)
os.unlink(tmp_fa + '.fai')
return score
def test_get_total_alignment_score(self):
'''Test get_total_alignment_score'''
bam = os.path.join(data_dir,
'mapping_test_get_total_alignment_score.bam')
expected = 219
got = mapping.get_total_alignment_score(bam)
self.assertEqual(got, expected)
def _total_alignment_score(self, seq_name):
tmpdir = tempfile.mkdtemp(prefix='tmp.get_total_aln_score.', dir=os.getcwd())
tmp_bam = os.path.join(tmpdir, 'tmp.get_total_alignment_score.bam')
tmp_fa = os.path.join(tmpdir, 'tmp.get_total_alignment_score.ref.fa')
faidx.write_fa_subset(
[seq_name],
self.references_fa,
tmp_fa,
samtools_exe=self.samtools_exe,
verbose=True,
verbose_filehandle=self.log_fh
)
mapping.run_bowtie2(
self.reads1,
self.reads2,
tmp_fa,
tmp_bam[:-4],
threads=self.threads,
samtools=self.samtools_exe,
bowtie2=self.bowtie2_exe,
bowtie2_preset=self.bowtie2_preset,
verbose=True,
verbose_filehandle=self.log_fh
)
score = mapping.get_total_alignment_score(tmp_bam)
shutil.rmtree(tmpdir)
return score
def _get_total_alignment_score(self, gene_name):
tmp_bam = os.path.join(self.root_dir, 'tmp.get_total_alignment_score.bam')
assert not os.path.exists(tmp_bam)
tmp_fa = os.path.join(self.root_dir, 'tmp.get_total_alignment_score.ref.fa')
assert not os.path.exists(tmp_fa)
faidx.write_fa_subset([gene_name], self.genes_fa, tmp_fa, samtools_exe=self.samtools_exe, verbose=self.verbose)
mapping.run_bowtie2(
self.reads1,
self.reads2,
tmp_fa,
tmp_bam[:-4],
threads=self.threads,
samtools=self.samtools_exe,
bowtie2=self.bowtie2_exe,
bowtie2_preset=self.bowtie2_preset,
verbose=self.verbose,
)
score = mapping.get_total_alignment_score(tmp_bam)
os.unlink(tmp_bam)
os.unlink(tmp_fa)
os.unlink(tmp_fa + '.fai')
return score
def test_get_total_alignment_score(self):
'''Test get_total_alignment_score'''
bam = os.path.join(data_dir, 'mapping_test_get_total_alignment_score.bam')
expected = 219
got = mapping.get_total_alignment_score(bam)
self.assertEqual(got, expected)
