def analyseRecombindationResults(self,oligoReport,featureList,outputFile="oligo_recomb_analysis.txt"): result = Report() result.extend(oligoReport) rowNames = oligoReport.returnRowNames() recordAlignment = SeqRecord(Seq("")) recordAlignment.features = featureList for rName in rowNames: output.write(rName + "\n") start = float(oligoReport["genomic_start"][rName]) end = float(oligoReport["genomic_end"][rName]) oligo = oligoReport["best"][rName] keyString = "\n(%s,%s) %s\n\n" % (start,end,oligo) output.write(keyString) subFeatures = self._selectFeatures(featureList,start,end) index = 0 for feature in subFeatures: matchName = "match_" + str(index) id = feature.id qValue = feature.qualifiers["query"] sValue = feature.qualifiers["subject"] matchString = feature.qualifiers["alignment"] output.write(id + "\n") output.write(matchString + "\n\n") result.add(rName,matchName,qValue) index += 1 output.close() return result