def createVcfHeader(self, m, commentString=""): """Create the VCF Header using a simple template. """ sourceConfigFP = ConfigUtils.createTemplateFP("tcgaVCF1.1Header.template") sHeaderTemplate = Template(sourceConfigFP.read()) missingAnnotations = [] headerSubKeys = dict() for reqHdr in TcgaVcfOutputRenderer.requiredHeaderAnnotations: if reqHdr not in m.keys(): missingAnnotations.append(reqHdr) headerSubKeys[reqHdr] = "." else: headerSubKeys[reqHdr] = m[reqHdr] headerSubKeys['date'] = str(datetime.now().date()).replace('-', '') headerSubKeys['comments'] = commentString headerSubKeys['tumor_subtype_upper'] = headerSubKeys['tumor_subtype'].upper() sHeader = sHeaderTemplate.safe_substitute(headerSubKeys) return sHeader
def createVcfHeader(self, m, commentString=""): """Create the VCF Header using a simple template. """ sourceConfigFP = ConfigUtils.createTemplateFP( "tcgaVCF1.1Header.template") sHeaderTemplate = Template(sourceConfigFP.read()) missingAnnotations = [] headerSubKeys = dict() for reqHdr in TcgaVcfOutputRenderer.requiredHeaderAnnotations: if reqHdr not in m.keys(): missingAnnotations.append(reqHdr) headerSubKeys[reqHdr] = "." else: headerSubKeys[reqHdr] = m[reqHdr] headerSubKeys['date'] = str(datetime.now().date()).replace('-', '') headerSubKeys['comments'] = commentString headerSubKeys['tumor_subtype_upper'] = headerSubKeys[ 'tumor_subtype'].upper() sHeader = sHeaderTemplate.safe_substitute(headerSubKeys) return sHeader