def app_profile_msi(*args, **kwargs):
logger.getLogger(__name__)
app_name = "cancersig profile msi"
raw_msisensor_out = kwargs['raw_msisensor_out']
raw_msisensor_out_somatic = kwargs['raw_msisensor_out_somatic']
sample_id = kwargs['sample_id']
output_file = kwargs['output_file']
disp.new_section_txt("S T A R T < " + app_name + " >")
required_params = OrderedDict()
required_params[
'msisensor output (--raw_msisensor_out)'] = raw_msisensor_out
required_params[
'msisensor somatic (--raw_msisensor_out_somatic)'] = raw_msisensor_out_somatic
required_params['sample id (--sample_id)'] = sample_id
required_params['output file name (-o/--output_file)'] = output_file
optional_params = OrderedDict()
disp.show_config(
app_description=APP_PROFILE_MSI_DESCRIPTION,
required_params=required_params,
optional_params=optional_params,
)
disp.new_section_txt("E X E C U T E < " + app_name + " >")
msi_profiler = MSIProfiler()
msi_profiler.profile(
raw_msisensor_out,
raw_msisensor_out_somatic,
sample_id,
output_file,
)
logger.getLogger(__name__)
disp.new_section_txt("F I N I S H < " + app_name + " >")
def app_profile_sv(*args, **kwargs):
logger.getLogger(__name__)
app_name = "cancersig profile sv"
input_vcf_file = kwargs['input_vcf_file']
output_file = kwargs['output_file']
sample_id = kwargs['sample_id']
disp.new_section_txt("S T A R T < " + app_name + " >")
required_params = OrderedDict()
required_params[
'input vcf file name (-i/--input_vcf_file)'] = input_vcf_file
required_params['output file name (-o/--output_file)'] = output_file
optional_params = OrderedDict()
optional_params['sample id (--sample_id)'] = sample_id
disp.show_config(
app_description=APP_PROFILE_SV_DESCRIPTION,
required_params=required_params,
optional_params=optional_params,
)
disp.new_section_txt("E X E C U T E < " + app_name + " >")
sv_profiler = SVProfiler()
sv_profiler.profile(
input_vcf_file,
output_file,
sample_id,
)
logger.getLogger(__name__)
disp.new_section_txt("F I N I S H < " + app_name + " >")
def app_profile_snv(*args, **kwargs):
logger.getLogger(__name__)
app_name = "cancersig profile snv"
input_vcf_file = kwargs['input_vcf_file']
ref_genome_file = kwargs['ref_genome_file']
output_file = kwargs['output_file']
gt_format = kwargs['gt_format']
sample_id = kwargs['sample_id']
disp.new_section_txt("S T A R T < " + app_name + " >")
required_params = OrderedDict()
required_params[
'input vcf file name (-i/--input_vcf_file)'] = input_vcf_file
required_params['reference genome (-r/--reference)'] = ref_genome_file
required_params['output file name (-o/--output_file)'] = output_file
optional_params = OrderedDict()
optional_params['sample id (--sample_id)'] = sample_id
optional_params['genotype format (-g/--gt_format)'] = gt_format
disp.show_config(
app_description=APP_PROFILE_SNV_DESCRIPTION,
required_params=required_params,
optional_params=optional_params,
)
disp.new_section_txt("E X E C U T E < " + app_name + " >")
snv_profiler = SNVProfiler()
snv_profiler.profile(
input_vcf_file,
ref_genome_file,
output_file,
gt_format,
sample_id,
)
logger.getLogger(__name__)
disp.new_section_txt("F I N I S H < " + app_name + " >")
def app_profile_merge(*args, **kwargs):
logger.getLogger(__name__)
app_name = "cancersig profile merge"
input_dirs = kwargs['input_dirs'].split(",")
output_file = kwargs['output_file']
profile_types = kwargs['profile_types']
disp.new_section_txt("S T A R T < " + app_name + " >")
required_params = OrderedDict()
required_params['input directories (-i/--input_dirs)'] = input_dirs
required_params['output file name (-o/--output_file)'] = output_file
optional_params = OrderedDict()
optional_params[
'profile types to be merged (--profile_types)'] = profile_types
disp.show_config(
app_description=APP_PROFILE_MERGE_DESCRIPTION,
required_params=required_params,
optional_params=optional_params,
)
disp.new_section_txt("E X E C U T E < " + app_name + " >")
profile_merger = ProfileMerger()
profile_merger.merge(
input_dirs,
output_file,
profile_types,
)
logger.getLogger(__name__)
disp.new_section_txt("F I N I S H < " + app_name + " >")
def app_signature_visualize(*args, **kwargs):
logger.getLogger(__name__)
app_name = "cancersig signature visualize"
mutation_profiles = kwargs['mutation_profiles']
signatures_probabilities = kwargs['signatures_probabilities']
output_dir = kwargs['output_dir']
disp.new_section_txt("S T A R T < " + app_name + " >")
required_params = OrderedDict()
required_params['input mutation profiles (-i/--mutation_profiles)'] = mutation_profiles
required_params['deciphered cancer signatures probabilities (--signatures_probabilities)'] = signatures_probabilities
required_params['output directory (-o/--output_dir)'] = output_dir
optional_params = OrderedDict()
disp.show_config(app_description=APP_SIGNATURE_VISUALIZE_DESCRIPTION,
required_params=required_params,
optional_params=optional_params,
)
disp.new_section_txt("E X E C U T E < " + app_name + " >")
vz = Visualizer()
vz.visualize(mutation_profiles,
signatures_probabilities,
output_dir,
)
logger.getLogger(__name__)
disp.new_section_txt("F I N I S H < " + app_name + " >")
def app_signature_decipher(*args, **kwargs):
logger.getLogger(__name__)
app_name = "cancersig signature decipher"
mutation_profiles = kwargs['mutation_profiles']
output_prefix = kwargs['output_prefix']
min_signatures = kwargs['min_signatures']
max_signatures = kwargs['max_signatures']
disp.new_section_txt("S T A R T < " + app_name + " >")
required_params = OrderedDict()
required_params['input mutation profiles (-i/--mutation_profiles)'] = mutation_profiles
required_params['output file prefix (-o/--output_prefix)'] = output_prefix
optional_params = OrderedDict()
optional_params['minimum number of signatures (--min_signatures)'] = min_signatures
optional_params['maximum number of signatures (--max_signatures)'] = max_signatures
disp.show_config(app_description=APP_SIGNATURE_DECIPHER_DESCRIPTION,
required_params=required_params,
optional_params=optional_params,
)
disp.new_section_txt("E X E C U T E < " + app_name + " >")
cancersig_nmf_controller = CancerSigNMFController()
cancersig_nmf_controller.decipher(mutation_profiles,
output_prefix,
min_signatures,
max_signatures,
)
logger.getLogger(__name__)
disp.new_section_txt("F I N I S H < " + app_name + " >")
def throw(self, err_msg=""):
frm = inspect.stack()[1]
mod = inspect.getmodule(frm[0])
logger.getLogger(mod.__name__)
logger.throw(err_msg)
def warning(self, warning_msg=""):
frm = inspect.stack()[1]
mod = inspect.getmodule(frm[0])
logger.getLogger(mod.__name__)
logger.warning(warning_msg)
def info(self, info_msg=""):
if self.__verbose:
frm = inspect.stack()[1]
mod = inspect.getmodule(frm[0])
logger.getLogger(mod.__name__)
logger.info(info_msg)
def dbg(self, dbg_msg=""):
if self.__debug_mode:
frm = inspect.stack()[1]
mod = inspect.getmodule(frm[0])
logger.getLogger(mod.__name__)
logger.dbg(dbg_msg)
