diff --git a/iAnnotateSV/AnnotationForKinaseDomain.py b/iAnnotateSV/AnnotationForKinaseDomain.py index 26218cd..030f4da 100644 --- a/iAnnotateSV/AnnotationForKinaseDomain.py +++ b/iAnnotateSV/AnnotationForKinaseDomain.py @@ -128,10 +128,10 @@ def run(svDFA, refPath, ctPath, allctPath, upPath, verbose): def processData(chrom, transcript, refDF, upDF): transcripts = (refDF[refDF['name'] == transcript]) if (len(transcripts) > 1): - transcriptIdx, = (transcripts[transcripts['chrom'] == chrom].index) + transcriptIdx = getValueOrDefault(transcripts[transcripts['chrom'] == chrom].index,0) else: try: - transcriptIdx, = (refDF[refDF['name'] == transcript].index) + transcriptIdx = getValueOrDefault(refDF[refDF['name'] == transcript].index,0) except ValueError: return (None, None, None) @@ -284,3 +284,13 @@ def getKinaseInfo(chrom, pos, gene, egene1, egene2, transcript, refDF, upDF): kanno = "Kinase Domain Not Included" # print gene, pos, chromStart, chromEnd, transcript, strand, kanno return(kanno) + +def getValueOrDefault(value, index, default=None): + returnValue = default + + try: + returnValue = value[index] + except Exception: + pass + + return returnValue