def cmpH5Summarize(inCmp, movieSummary=True, refSummary=True): """Summarize a cmp.h5 file""" reader = CmpH5Reader(inCmp) tstr = "filename: %s\nversion: %s\nn reads: %d\nn refs: " + \ "%d\nn movies: %d\nn bases: %d\navg rl: %d\navg acc: %g" rl, acc, mov = zip(*[(r.readLength, r.accuracy, r.movieInfo[0]) for r in reader]) summaryStr = ( tstr % (os.path.basename(reader.file.filename), reader.version, len(reader), len(reader.referenceInfoTable), len(set(mov)), NP.sum(rl), NP.round(NP.mean(rl)), NP.round(NP.mean(acc), 4))) eTbl = Tbl(nBases=Sum(ReadLength), avgReadLength=Mean(ReadLength), avgAccuracy=Mean(Accuracy)) movieSummaryTxt = rec2txt(toRecArray( query(reader, what=eTbl, groupBy=Movie)), padding=5, precision=1) refSummaryTxt = rec2txt(toRecArray( query(reader, what=eTbl, groupBy=Reference)), padding=5, precision=1) return (summaryStr + ("\n\n\t Movie Summary:\n" + (movieSummaryTxt if movieSummary else "\n")) + ("\n\n\t Reference Summary:\n" + (refSummaryTxt if refSummary else "\n")))
def cmpH5Summarize(inCmp, movieSummary = True, refSummary = True): """Summarize a cmp.h5 file""" reader = CmpH5Reader(inCmp) tstr = "filename: %s\nversion: %s\nn reads: %d\nn refs: " + \ "%d\nn movies: %d\nn bases: %d\navg rl: %d\navg acc: %g" rl,acc,mov = zip(*[(r.readLength,r.accuracy,r.movieInfo[0]) for r in reader ]) summaryStr = (tstr % (os.path.basename(reader.file.filename), reader.version, len(reader), len(reader.referenceInfoTable), len(set(mov)), NP.sum(rl), NP.round(NP.mean(rl)), NP.round(NP.mean(acc), 4))) eTbl = Tbl(nBases = Sum(ReadLength), avgReadLength = Mean(ReadLength), avgAccuracy = Mean(Accuracy)) movieSummaryTxt = rec2txt(toRecArray(query(reader, what = eTbl, groupBy = Movie)), padding = 5, precision = 1) refSummaryTxt = rec2txt(toRecArray(query(reader, what = eTbl, groupBy = Reference)), padding = 5, precision = 1) return (summaryStr + ("\n\n\t Movie Summary:\n" + (movieSummaryTxt if movieSummary else "\n")) + ("\n\n\t Reference Summary:\n" + (refSummaryTxt if refSummary else "\n")))
def prettyPrint(res): print rec2txt(res, padding = 20, precision = 2)
def prettyPrint(res): print rec2txt(res, padding=20, precision=2)