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
