Example #1
0
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 + " >")
Example #2
0
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 + " >")
Example #3
0
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 + " >")
Example #4
0
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 + " >")
Example #5
0
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 + " >")
Example #6
0
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 + " >")