diff --git a/AnnotatorCore.py b/AnnotatorCore.py index f0b4fca..a448a7d 100644 --- a/AnnotatorCore.py +++ b/AnnotatorCore.py @@ -1286,7 +1286,7 @@ def process_clinical_data(annotatedmutfiles, clinicalfile, outfile): outf.write('\tHIGHEST_PX_LEVEL') outf.write( '\tONCOGENIC_MUTATIONS\t#ONCOGENIC_MUTATIONS\tRESISTANCE_MUTATIONS\t#RESISTANCE_MUTATIONS\t#MUTATIONS_WITH_SENSITIVE_THERAPEUTIC_IMPLICATIONS\t#MUTATIONS_WITH_RESISTANCE_THERAPEUTIC_IMPLICATIONS\t#MUTATIONS_WITH_DIAGNOSTIC_IMPLICATIONS\t#MUTATIONS_WITH_PROGNOSTIC_IMPLICATIONS\t#MUTATIONS\n') - isample = headers['SAMPLE_ID'] + isample = geIndexOfHeader(headers, SAMPLE_HEADERS) for row in reader: sample = row[isample] @@ -1912,8 +1912,8 @@ def readCancerTypes(clinicalFile, data): reader = csv.reader(infile, delimiter='\t') headers = readheaders(reader) - iSample = geIndexOfHeader(headers, ['SAMPLE_ID']) - iCancerType = geIndexOfHeader(headers, ['ONCOTREE_CODE', 'CANCER_TYPE']) + iSample = geIndexOfHeader(headers, SAMPLE_HEADERS) + iCancerType = geIndexOfHeader(headers, CANCER_TYPE_HEADERS) for row in reader: data[row[iSample]] = row[iCancerType]