Пример #1
0
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")))
Пример #2
0
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")))
Пример #3
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def prettyPrint(res):
    print rec2txt(res, padding = 20, precision = 2)
Пример #4
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def prettyPrint(res):
    print rec2txt(res, padding=20, precision=2)