def test_bwa_mem_single():
# Define mock snakemake object.
snakemake = MockSnakemake({
'input': {
'reference': 'reference/hg38/hg38.fasta',
'reads': ['test.fastq.gz'],
},
'output': {
'bam': 'test.bam',
},
'params': {
'extra': '',
},
'log': 'logs/bwa_mem/test.log',
'threads': 12,
})
expected_command = '( bwa mem reference/hg38/hg38 test.fastq.gz -t 12 | samtools view -Sb - > test.bam ) 2> logs/bwa_mem/test.log'
# Define files.
reference = sw.SimpleTemplateFile('reference')
read = sw.SimpleTemplateFile('reads')
bam = sw.SimpleTemplateFile('bam')
# Define input, output, parameters and threads.
input = sw.SimpleRuleInput({
'reference':
Parameter(f=reference, option=None, used=False),
'reads': [Parameter(f=read, option=None)],
})
output = sw.SimpleRuleOutput({
'bam':
Parameter(f=bam, option=None, used=True, redirected=True),
})
threads = sw.SimpleRuleThreads(command_key='-t')
params = sw.SimpleRuleParams(
extra=True,
db_prefix=Parameter(
f=lambda sn: os.path.splitext(sn.input.reference)[0],
option=None,
priority=1),
pipe_command=Parameter(f=lambda sn: '| samtools view -Sb -'
if sn.output.bam.endswith('.bam') else '',
option=None,
priority=100))
wrapper = sw.Wrapper(
snakemake=snakemake,
command='bwa mem',
input=input,
output=output,
threads=threads,
params=params,
)
assert wrapper.shell_command() == expected_command
def test_samtools_sort_with_extra():
snakemake = MockSnakemake({
'input': {
'bam': 'test.bam'
},
'output': {
'sorted_bam': 'test.sorted.bam'
},
'params': {
'extra': '-l 9'
},
'log': 'logs/samtools_sort/test.log',
})
bam = sw.SimpleTemplateFile('bam')
sorted_bam = sw.SimpleTemplateFile('sorted_bam')
# Create RuleInput object.
input = sw.SimpleRuleInput({
'bam': Parameter(f=bam, option=None),
})
# Create RuleOutput object.
output = sw.SimpleRuleOutput({
'sorted_bam': [Parameter(f=sorted_bam, option='-o')],
})
# Create RuleParams object.
params = sw.SimpleRuleParams(
extra=True,
prefix=Parameter(
f=lambda sn: os.path.splitext(sn.output.sorted_bam)[0],
option='-T'))
# Create RuleThreads object.
threads = sw.SimpleRuleThreads(command_key='-@')
wrapper = sw.Wrapper(
snakemake,
command='samtools sort',
input=input,
output=output,
params=params,
threads=threads,
)
expected_shell_command = '( samtools sort test.bam -o test.sorted.bam -l 9 -T test.sorted -@ 1 ) 2> logs/samtools_sort/test.log'
assert wrapper.shell_command() == expected_shell_command
wrapper.run()
def test_bismark_genome_preparation():
# Define mock snakemake object.
snakemake = MockSnakemake({
'input': {
'reference_dir': 'reference/hg38',
},
'output': {
'bisulfite_genome_dir': 'reference/hg38/Bisulfite_Genome'
},
'params': {
'extra': '',
},
'log': 'logs/bismark_genome_preparation/log.log'
})
# Define files.
reference_dir = sw.SimpleTemplateDirectory('reference_dir')
bisulfite_genome_dir = sw.SimpleTemplateDirectory('bisulfite_genome_dir')
# Define input, output, and parameters.
input = sw.SimpleRuleInput({
'reference_dir': Parameter(reference_dir, None),
})
output = sw.SimpleRuleOutput({
'bisulfite_genome_dir':
Parameter(bisulfite_genome_dir, None, False),
})
params = sw.SimpleRuleParams(extra=True)
wrapper = sw.Wrapper(
snakemake=snakemake,
command='bismark_genome_preparation',
input=input,
output=output,
params=params,
)
assert wrapper.shell_command(
) == '( bismark_genome_preparation reference/hg38 ) 2> logs/bismark_genome_preparation/log.log'
def assign(self, snakemake):
if self.include_extra:
self.extra = snakemake.params.extra
for key, parameter in self.params.items():
if callable(parameter.f):
self.params[key] = Parameter(
self._infer_parameter_with_function(parameter.f, snakemake),
parameter.option,
parameter.used,
parameter.redirected,
parameter.priority
)
def test_bismark_paired_with_zipped_fastq():
snakemake = MockSnakemake({
'input': {
'fastq': ['data/test.read1.fastq.gz', 'data/test.read2.fastq.gz'],
'reference_dir': 'reference/hg38_bismark',
'bisulfite_genome_dir': 'reference/hg38_bismark/Bisulfite_Genome',
},
'output': {
'bam': 'result/test.bismark.bam',
'report': 'result/test.bismark_report.txt',
},
'wildcards': {
'sample': 'test',
},
'threads': 6,
'params': {
'extra': '--bowtie1'
},
'log': 'logs/bismark/test.log',
})
# Define files.
read1 = sw.SimpleTemplateFile('fastq')
read2 = sw.SimpleTemplateFile('fastq')
reference_dir = sw.SimpleTemplateDirectory('reference_dir')
bisulfite_genome_dir = sw.SimpleTemplateDirectory('bisulfite_genome_dir')
bam = sw.RenamedTemplateFile(
name='bam',
regex=r'(?P<prefix>.+?).bismark.bam',
raw_name='{prefix}.read1_bismark_bt2_pe.bam',
)
report = sw.RenamedTemplateFile(
name='report',
regex=r'(?P<prefix>.+?).bismark_report.txt',
raw_name='{prefix}.read1_bismark_bt2_PE_report.txt')
input = sw.SimpleRuleInput({
'reference_dir':
Parameter(reference_dir, None),
'fastq': [Parameter(read1, '-1'),
Parameter(read2, '-2')],
'bisulfite_genome_dir':
Parameter(bisulfite_genome_dir, None, False)
})
output = sw.SimpleRuleOutput({
'bam': Parameter(bam, None, False),
'report': Parameter(report, None, False),
})
params = sw.SimpleRuleParams(extra=True,
outdir=Parameter(
lambda sn: os.path.dirname(sn.output.bam),
'-o', True))
threads = sw.ScaledRuleThreads(
command_key='--multicore',
scale=lambda sn: 1 / 2 if '--bowtie1' in sn.params.extra else 1 / 3)
wrapper = sw.Wrapper(
snakemake,
command='bismark',
input=input,
output=output,
params=params,
threads=threads,
)
assert wrapper.shell_command() == \
'( bismark reference/hg38_bismark ' \
'-1 data/test.read1.fastq.gz -2 data/test.read2.fastq.gz '\
'--bowtie1 ' \
'-o result ' \
'--multicore 3 ' \
'&& mv result/test.read1_bismark_bt2_pe.bam result/test.bismark.bam ' \
'&& mv result/test.read1_bismark_bt2_PE_report.txt result/test.bismark_report.txt ' \
') 2> logs/bismark/test.log' \
def test_bismark_single_with_unzipped_fastq_bowtie1():
snakemake = MockSnakemake({
'input': {
'fastq': 'data/test.fastq',
'reference_dir': 'reference/hg38_bismark',
'bisulfite_genome_dir': 'reference/hg38_bismark/Bisulfite_Genome',
},
'output': {
'bam': 'result/test.bismark.bam',
'report': 'result/test.bismark_report.txt',
},
'wildcards': {
'sample': 'test',
},
'threads': 6,
'params': {
'extra': '--bowtie1'
},
'log': 'logs/bismark/test.log',
})
# Define files.
fastq = sw.SimpleTemplateFile('fastq')
reference_dir = sw.SimpleTemplateDirectory('reference_dir')
bisulfite_genome_dir = sw.SimpleTemplateDirectory('bisulfite_genome_dir')
bam = sw.RenamedTemplateFile(
name='bam',
regex=r'(?P<prefix>.+?).bismark.bam',
raw_name='{prefix}_bismark_bt2.bam',
)
report = sw.RenamedTemplateFile(
name='report',
regex=r'(?P<prefix>.+?).bismark_report.txt',
raw_name='{prefix}_bismark_bt2_SE_report.txt')
# Define input, output, parameters, threads.
input = sw.SimpleRuleInput({
'reference_dir':
Parameter(f=reference_dir, option=None),
'fastq':
Parameter(f=fastq, option=None),
'bisulfite_genome_dir':
Parameter(f=bisulfite_genome_dir, option=None, used=False),
})
output = sw.SimpleRuleOutput({
'bam':
Parameter(f=bam, option=None, used=False),
'report':
Parameter(f=report, option=None, used=False),
})
params = sw.SimpleRuleParams(extra=True,
outdir=Parameter(
lambda sn: os.path.dirname(sn.output.bam),
'-o', True))
threads = sw.ScaledRuleThreads(
command_key='--multicore',
scale=lambda sn: 1 / 2 if '--bowtie1' in sn.params.extra else 1 / 3)
wrapper = sw.Wrapper(
snakemake,
command='bismark',
input=input,
output=output,
params=params,
threads=threads,
)
assert bam.rename_command(
) == 'mv result/test_bismark_bt2.bam result/test.bismark.bam'
assert report.rename_command(
) == 'mv result/test_bismark_bt2_SE_report.txt result/test.bismark_report.txt'
assert wrapper.shell_command() == \
'( bismark reference/hg38_bismark data/test.fastq '\
'--bowtie1 ' \
'-o result ' \
'--multicore 3 ' \
'&& mv result/test_bismark_bt2.bam result/test.bismark.bam ' \
'&& mv result/test_bismark_bt2_SE_report.txt result/test.bismark_report.txt ' \
') 2> logs/bismark/test.log' \