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
