diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py index e088a31..19cfa0f 100644 --- a/gene_splicer/utils.py +++ b/gene_splicer/utils.py @@ -391,19 +391,6 @@ def align(target_seq, else: return alignment_path - -HIVINTACT_TRANSLATION_TABLE = { - 'APOBECHypermutationDetected': 'Hypermut', - 'LongDeletion': 'LargeDeletion', - 'PackagingSignalDeletion': '5DEFECT', - 'PackagingSignalNotComplete': '5DEFECT', - 'MajorSpliceDonorSiteMutated': '5DEFECT', - 'WrongORFNumber': 'PrematureStop_OR_AAtooLong_OR_AAtooShort', - } - -def translate_hivintact_error(error): - return HIVINTACT_TRANSLATION_TABLE.get(error, error) - HIVINTACT_ERRORS_TABLE = [ 'NonHIV', 'LongDeletion', @@ -427,7 +414,7 @@ def iterate_hivintact_data(name, outpath): def get_verdict(SEQID, all_errors): ordered = sorted(all_errors, key=HIVINTACT_ERRORS_TABLE.index) - verdict = translate_hivintact_error(ordered[0]) + verdict = ordered[0] return [SEQID, verdict] for d in glob.glob(str(outpath / 'hivintact*')):