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Support Tumor_Sample_Barcode as column name in clinical file #215

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merged 1 commit into from
Feb 14, 2024
Merged

Support Tumor_Sample_Barcode as column name in clinical file #215

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6 changes: 3 additions & 3 deletions AnnotatorCore.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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]
Expand Down Expand Up @@ -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]
Expand Down