def macs(resource, use_background=True, p_value=None):
"""Run ``MACS 1.4`` process on the resource.
This method runs `MACS 1.4`_ process with ``p-value`` specified in
arguments and ``bam`` file from the sample.
If ``use_background`` argument is set to ``True``, ``bam`` file from
background sample is passed to the process as the control. Mappable
genome size is taken from the sample annotation.
.. _MACS 1.4:
http://resolwe-bio.readthedocs.io/en/latest/catalog-definitions.html#process-macs14
:param bool use_background: if set to ``True``, background sample
will be used in the process
:param float p_value: p-value used in the process
"""
inputs = {}
if p_value is not None:
inputs['pvalue'] = p_value
results = []
if not isinstance(resource, list):
resource = [resource]
for single_resource in resource:
background_filter = {}
if use_background:
collection_id = get_resource_collection(single_resource)
if collection_id:
background_filter['collection'] = collection_id
for sample in get_samples(single_resource):
inputs['treatment'] = sample.get_bam().id
try:
inputs['gsize'] = gsize_organism(
sample.descriptor['sample']['organism'])
except KeyError:
raise KeyError('{} is not annotated'.format(sample))
if use_background:
if is_background(sample) and not is_sample(single_resource):
# Don't run process on the background sample,
# but let it fail if it is run directly on sample
continue
background = sample.get_background(**background_filter)
inputs['control'] = background.get_bam().id
macs_obj = sample.resolwe.get_or_run(slug='macs14', input=inputs)
sample.add_data(macs_obj)
results.append(macs_obj)
return results
def macs(resource, use_background=True, p_value=None):
"""Run ``MACS 1.4`` process on the resource.
This method runs `MACS 1.4`_ process with ``p-value`` specified in
arguments and ``bam`` file from the sample.
If ``use_background`` argument is set to ``True``, ``bam`` file from
background sample is passed to the process as the control.
.. _MACS 1.4:
http://resolwe-bio.readthedocs.io/en/latest/catalog-definitions.html#process-macs14
:param bool use_background: if set to ``True``, background sample
will be used in the process
:param float p_value: p-value used in the process
"""
inputs = {}
if p_value is not None:
inputs['pvalue'] = p_value
results = []
if not isinstance(resource, list):
resource = [resource]
for single_resource in resource:
background_filter = {}
if use_background:
collection_id = get_resource_collection(single_resource)
if collection_id:
background_filter['collection'] = collection_id
for sample in get_samples(single_resource):
inputs['treatment'] = sample.get_primary_bam(fallback_to_bam=True).id
if use_background:
if sample.is_background and not is_sample(single_resource):
# Don't run process on the background sample,
# but let it fail if it is run directly on sample
continue
background = sample.get_background(**background_filter)
inputs['control'] = background.get_primary_bam(fallback_to_bam=True).id
macs_obj = sample.resolwe.get_or_run(slug='macs14', input=inputs)
sample.add_data(macs_obj)
results.append(macs_obj)
return results
def rose2(resource, use_background=True, tss=None, stitch=None, beds=None):
"""Run ``ROSE 2`` process on the resource.
This method runs `ROSE2`_ process with ``tss_exclusion`` and
``stitch`` parameters specified in arguments.
Separate process is run for each bed file on the sample. To run
process only on subset of those files, list them in ``beds``
argument (if only one object is given, it will be auto-wrapped in
list, if it is not already).
If ``use_background`` argument is set to ``True``, bam file from
background sample is passed to the process as the control.
.. _ROSE2:
http://resolwe-bio.readthedocs.io/en/latest/catalog-definitions.html#process-rose2
:param bool use_background: if set to ``True``, background sample
will be used in the process
:param int tss: TSS exclusion used in process
:param int stitch: Stitch used in process
:param list beds: subset of bed files to run process on, if empty
processes for all bed files will be run
"""
results = []
if not isinstance(resource, list):
resource = [resource]
for single_resource in resource:
background_filter = {}
if use_background:
collection_id = get_resource_collection(single_resource)
if collection_id:
background_filter['collection'] = collection_id
for sample in get_samples(single_resource):
inputs = {
'rankby': sample.get_bam().id,
}
if tss is not None:
inputs['tss'] = tss
if stitch is not None:
inputs['stitch'] = stitch
if use_background:
if sample.is_background and not is_sample(single_resource):
# Don't run process on the background sample,
# but let it fail if it is run directly on sample
continue
background = sample.get_background(**background_filter)
inputs['control'] = background.get_bam().id
bed_list = sample.get_macs()
if beds is not None:
# Convert objects to the list of their ids
if isinstance(beds, list):
bed_filter = [get_data_id(bed) for bed in beds]
else:
bed_filter = [get_data_id(beds)]
bed_list = bed_list.filter(id__in=bed_filter)
for bed in bed_list:
inputs['input'] = bed.id
rose = sample.resolwe.get_or_run(slug='rose2', input=inputs)
sample.add_data(rose)
results.append(rose)
return results
def rose2(resource, use_background=True, tss=None, stitch=None, beds=None):
"""Run ``ROSE 2`` process on the resource.
This method runs `ROSE2`_ process with ``tss_exclusion`` and
``stitch`` parameters specified in arguments.
Separate process is run for each bed file on the sample. To run
process only on subset of those files, list them in ``beds``
argument (if only one object is given, it will be auto-wrapped in
list, if it is not already).
If ``use_background`` argument is set to ``True``, bam file from
background sample is passed to the process as the control.
.. _ROSE2:
http://resolwe-bio.readthedocs.io/en/latest/catalog-definitions.html#process-rose2
:param bool use_background: if set to ``True``, background sample
will be used in the process
:param int tss: TSS exclusion used in process
:param int stitch: Stitch used in process
:param list beds: subset of bed files to run process on, if empty
processes for all bed files will be run
"""
results = []
if not isinstance(resource, list):
resource = [resource]
for single_resource in resource:
background_filter = {}
if use_background:
collection_id = get_resource_collection(single_resource)
if collection_id:
background_filter['collection'] = collection_id
for sample in get_samples(single_resource):
inputs = {
'rankby': sample.get_bam().id,
}
if tss is not None:
inputs['tss'] = tss
if stitch is not None:
inputs['stitch'] = stitch
if use_background:
if sample.is_background and not is_sample(single_resource):
# Don't run process on the background sample,
# but let it fail if it is run directly on sample
continue
background = sample.get_background(**background_filter)
inputs['control'] = background.get_bam().id
bed_list = sample.get_macs()
if beds is not None:
# Convert objects to the list of their ids
if isinstance(beds, list):
bed_filter = [get_data_id(bed) for bed in beds]
else:
bed_filter = [get_data_id(beds)]
bed_list = bed_list.filter(id__in=bed_filter)
for bed in bed_list:
inputs['input'] = bed.id
rose = sample.resolwe.get_or_run(slug='rose2', input=inputs)
sample.add_data(rose)
results.append(rose)
return results