def _align(self, fastq_path, output_dir, fastq2_path=None):
# Gather default arguments.
sort_type = 'Unsorted' if self._external_sort else 'SortedByCoordinate'
args = {
'--twopassMode': ('Basic', ),
'--outReadsUnmapped': ('None', ),
'--outSAMtype': ('BAM', sort_type),
'--runThreadN': (self._threads, ),
'--chimSegmentMin': (self._min_flank, ),
'--outSAMstrandField': ('intronMotif', ) # XS field for Stringtie.
}
star_align(fastq_path=fastq_path,
fastq2_path=fastq2_path,
index_path=self._reference.index_path,
output_dir=output_dir,
extra_args=toolz.merge(args, self._extra_args))
# If not yet sorted, sort bam file using samtools/sambamba.
sorted_bam_path = output_dir / 'Aligned.sortedByCoord.out.bam'
if sort_type == 'Unsorted':
unsorted_bam_path = output_dir / 'Aligned.out.bam'
sort_bam(unsorted_bam_path, sorted_bam_path, threads=self._threads)
unsorted_bam_path.unlink()
def _align(self, fastq_path, output_dir, fastq2_path=None):
# Gather default arguments.
sort_type = 'Unsorted' if self._external_sort else 'SortedByCoordinate'
args = {
'--twopassMode': ('Basic', ),
'--outReadsUnmapped': ('None', ),
'--outSAMtype': ('BAM', sort_type),
'--runThreadN': (self._threads, ),
'--chimSegmentMin': (self._min_flank, ),
'--outSAMstrandField': ('intronMotif', ) # XS field for Stringtie.
}
star_align(
fastq_path=fastq_path,
fastq2_path=fastq2_path,
index_path=self._reference.index_path,
output_dir=output_dir,
extra_args=toolz.merge(args, self._extra_args))
# If not yet sorted, sort bam file using samtools/sambamba.
sorted_bam_path = output_dir / 'Aligned.sortedByCoord.out.bam'
if sort_type == 'Unsorted':
unsorted_bam_path = output_dir / 'Aligned.out.bam'
sort_bam(unsorted_bam_path, sorted_bam_path, threads=self._threads)
unsorted_bam_path.unlink()
def test_basic_call(self, mocker, star_align_kws):
"""Tests example call."""
mock_run = mocker.patch.object(star, 'run_command')
star.star_align(**star_align_kws)
mock_run.assert_called_once_with(args=[
'STAR', '--genomeDir', 'index', '--outFileNamePrefix',
str(star_align_kws['output_dir']) + '/', '--readFilesIn',
'sample.R1.fastq.gz', '--readFilesCommand', 'gunzip', '-c'
],
log_path=None)
def test_basic_call(self, mocker, star_align_kws):
"""Tests example call."""
mock_run = mocker.patch.object(star, 'run_command')
star.star_align(**star_align_kws)
mock_run.assert_called_once_with(
args=[
'STAR', '--genomeDir', 'index', '--outFileNamePrefix',
str(star_align_kws['output_dir']) + '/', '--readFilesIn',
'sample.R1.fastq.gz', '--readFilesCommand', 'gunzip', '-c'
],
log_path=None)
def test_basic_without_gzip(self, mocker, star_align_kws):
"""Tests example without gzipped input."""
mock_run = mocker.patch.object(star, 'run_command')
star_align_kws['fastq_path'] = Path('sample.R1.fastq')
star.star_align(**star_align_kws)
mock_run.assert_called_once_with(args=[
'STAR', '--genomeDir', 'index', '--outFileNamePrefix',
str(star_align_kws['output_dir']) + '/', '--readFilesIn',
'sample.R1.fastq'
],
log_path=None)
def test_basic_without_gzip(self, mocker, star_align_kws):
"""Tests example without gzipped input."""
mock_run = mocker.patch.object(star, 'run_command')
star_align_kws['fastq_path'] = Path('sample.R1.fastq')
star.star_align(**star_align_kws)
mock_run.assert_called_once_with(
args=[
'STAR', '--genomeDir', 'index', '--outFileNamePrefix',
str(star_align_kws['output_dir']) + '/', '--readFilesIn',
'sample.R1.fastq'
],
log_path=None)
def test_extra_arguments(self, mocker, star_align_kws):
"""Tests example call with extra arguments."""
mock_run = mocker.patch.object(star, 'run_command')
star_align_kws['extra_args'] = {'--outSAMtype': 'Unsorted'}
star.star_align(**star_align_kws)
mock_run.assert_called_once_with(args=[
'STAR', '--genomeDir', 'index', '--outFileNamePrefix',
str(star_align_kws['output_dir']) + '/', '--readFilesIn',
'sample.R1.fastq.gz', '--outSAMtype', 'Unsorted',
'--readFilesCommand', 'gunzip', '-c'
],
log_path=None)
def test_extra_arguments(self, mocker, star_align_kws):
"""Tests example call with extra arguments."""
mock_run = mocker.patch.object(star, 'run_command')
star_align_kws['extra_args'] = {'--outSAMtype': 'Unsorted'}
star.star_align(**star_align_kws)
mock_run.assert_called_once_with(
args=[
'STAR', '--genomeDir', 'index', '--outFileNamePrefix',
str(star_align_kws['output_dir']) + '/', '--readFilesIn',
'sample.R1.fastq.gz', '--outSAMtype', 'Unsorted',
'--readFilesCommand', 'gunzip', '-c'
],
log_path=None)