示例#1
0
def test_pileup():
    pe = PileupElement('A', 40)
    pe2 = PileupElement('A', 20)
    pe3 = PileupElement('G', None)
    pileup = Pileup([pe, pe2, pe3])
    assert pileup.bases() == ['A', 'A', 'G']
    assert pileup.quals() == [40, 20, None]
    assert pileup.most_common_base() == 'A'
示例#2
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    def merge(reads, max_qual=46, fraction_agree=0.75):
        """
        :type reads: list[pysam.AlignedSegment]
        :type max_qual: int
        :type fraction_agree: float
        :return: pysam.AlignedSegment
        """
        logging.debug("Merging {} read(s).".format(len(reads)))
        if len(reads) == 1:
            return reads[0]
        merged = reads[0]
        max_read_len = max([len(r.seq) for r in reads])
        new_seq = []
        new_quals = []
        for k in range(max_read_len):
            pileup = Pileup.from_reads(reads, k)
            merged_pileup_element = pileup.merge(max_qual, fraction_agree)
            new_seq.append(merged_pileup_element.base)
            new_quals.append(merged_pileup_element.phredqual())

        logging.debug("new seq is {}".format("".join(new_seq)))
        logging.debug("new qual is {}".format("".join(new_quals)))
        merged.seq = "".join(new_seq)
        merged.qual = "".join(new_quals)
        return merged
示例#3
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def test_merge():
    merged_pileup_elements = []
    """ :type: list[PileupElement] """
    pileups = []
    """ :type: list[Pileup] """
    reads = [my_read, my_read2, my_read3, my_read4]

    for k in range(0, 4):
        pile = Pileup.from_reads(reads, k)
        pileups.append(pile)
        merged_pileup_elements.append(pile.merge(max_qual=45, fraction_agree=0.75))

    # test that ties gives N
    assert merged_pileup_elements[0].base == 'N'  # tie, 2xA 2xG
    # test that majority vote works
    assert merged_pileup_elements[1].base == 'G'  # G wins from 3xG 1xA

    # test all 4 bases that were merged
    assert "".join([pe.base for pe in merged_pileup_elements]) == 'NGCT'
    # test that qualities were properly merged
    assert [pe.qual for pe in merged_pileup_elements] == [2, 45, 45, 45]
    # test that the size of each pileup works
    assert [len(p.bases()) for p in pileups] == [4, 4, 4, 3]

    assert ReadMerger.key(a) == ReadMerger.key(b)
    assert Pileup.from_reads([a, b], 0).merge(45, .75).base == 'N'
    assert Pileup.from_reads([a, b], 0).merge(45, .75).qual == 2
    assert Pileup.from_reads([a, b], 1).merge(45, .75).base == 'G'

    tmpfilename = tempfile.mkstemp('.bam')[1]
    outfile = pysam.AlignmentFile(tmpfilename, "wb", header=header)
    readmerger = ReadMerger([a, b], outfile, fraction_agree=0.75, max_qual=45, reads_between_logs=1)
    exitcode = readmerger.do_work()
    assert exitcode == 0
    metrics = readmerger.metrics.dict()
    assert 'L1' in metrics
    os.remove(tmpfilename)