Python SMCScoring Examples

Example #1

File: gentruth.py Project: Sage-Bionetworks/SMC-Het-Challenge

def getTruth3B(yml_ob,truth_vcf_prefix,vcf_location,filename=''):
	data_2 = getTruth2A(yml_ob,truth_vcf_prefix,vcf_location)
	cluster_assignments = SMCScoring.validate2Afor3A(data_2,data_2.count('\n')+1)
	data_3 = getTruth3A(yml_ob,truth_vcf_prefix,vcf_location)
	adm =  SMCScoring.validate3A(data_3,cluster_assignments,data_2.count('\n')+1)
	if filename:
		np.savetxt(filename,adm)
	return adm

Example #2

File: gentruth.py Project: asalcedo31/SMC-Het_Scoring

def getTruth3B(yml_ob, truth_vcf_prefix, vcf_location, filename=''):
    data_2 = getTruth2A(yml_ob, truth_vcf_prefix, vcf_location)
    cluster_assignments = SMCScoring.validate2Afor3A(data_2,
                                                     data_2.count('\n') + 1)
    data_3 = getTruth3A(yml_ob, truth_vcf_prefix, vcf_location)
    adm = SMCScoring.validate3A(data_3, cluster_assignments,
                                data_2.count('\n') + 1)
    if filename:
        np.savetxt(filename, adm)
    return adm

Example #3

File: gentruth.py Project: Sage-Bionetworks/SMC-Het-Challenge

def getTruth2B(yml_ob,truth_vcf_prefix,vcf_location,filename=''):
	data = getTruth2A(yml_ob,truth_vcf_prefix,vcf_location)
	ccm = SMCScoring.validate2A(data,data.count('\n')+1)
	if filename:
		np.savetxt(filename,ccm)
	return ccm

Example #4

File: gentruth.py Project: asalcedo31/SMC-Het_Scoring

def getTruth2B(yml_ob, truth_vcf_prefix, vcf_location, filename=''):
    data = getTruth2A(yml_ob, truth_vcf_prefix, vcf_location)
    ccm = SMCScoring.validate2A(data, data.count('\n') + 1)
    if filename:
        np.savetxt(filename, ccm)
    return ccm