Python ContigSet.consolidate方法代码示例

# 需要导入模块: from pbcore.io import ContigSet [as 别名]
# 或者: from pbcore.io.ContigSet import consolidate [as 别名]
    def test_contigset_consolidate_int_names(self):
        #build set to merge
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")

        inFas = os.path.join(outdir, 'infile.fasta')
        outFas1 = os.path.join(outdir, 'tempfile1.fasta')
        outFas2 = os.path.join(outdir, 'tempfile2.fasta')

        # copy fasta reference to hide fai and ensure FastaReader is used
        backticks('cp {i} {o}'.format(
                      i=ReferenceSet(data.getXml(9)).toExternalFiles()[0],
                      o=inFas))
        rs1 = ContigSet(inFas)

        double = 'B.cereus.1'
        exp_double = rs1.get_contig(double)

        # todo: modify the names first:
        with FastaWriter(outFas1) as writer:
            writer.writeRecord('5141', exp_double.sequence)
        with FastaWriter(outFas2) as writer:
            writer.writeRecord('5142', exp_double.sequence)

        exp_double_seqs = [exp_double.sequence, exp_double.sequence]
        exp_names = ['5141', '5142']

        obs_file = ContigSet(outFas1, outFas2)
        log.debug(obs_file.toExternalFiles())
        obs_file.consolidate()
        log.debug(obs_file.toExternalFiles())

        # open obs and compare to exp
        for name, seq in zip(exp_names, exp_double_seqs):
            self.assertEqual(obs_file.get_contig(name).sequence[:], seq)

# 需要导入模块: from pbcore.io import ContigSet [as 别名]
# 或者: from pbcore.io.ContigSet import consolidate [as 别名]
 def test_contigset_consolidate_genomic_consensus(self):
     """
     Verify that the contigs output by GenomicConsensus (e.g. quiver) can
     be consolidated.
     """
     FASTA1 = ("lambda_NEB3011_0_60",
         "GGGCGGCGACCTCGCGGGTTTTCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCG")
     FASTA2 = ("lambda_NEB3011_120_180",
         "CACTGAATCATGGCTTTATGACGTAACATCCGTTTGGGATGCGACTGCCACGGCCCCGTG")
     FASTA3 = ("lambda_NEB3011_60_120",
         "GTGGACTCGGAGCAGTTCGGCAGCCAGCAGGTGAGCCGTAATTATCATCTGCGCGGGCGT")
     files = []
     for i, (header, seq) in enumerate([FASTA1, FASTA2, FASTA3]):
         _files = []
         for suffix in ["", "|quiver", "|plurality", "|arrow", "|poa"]:
             tmpfile = tempfile.NamedTemporaryFile(suffix=".fasta").name
             with open(tmpfile, "w") as f:
                 f.write(">{h}{s}\n{q}".format(h=header, s=suffix, q=seq))
             _files.append(tmpfile)
         files.append(_files)
     for i in range(3):
         ds = ContigSet(*[f[i] for f in files])
         out1 = tempfile.NamedTemporaryFile(suffix=".contigset.xml").name
         fa1 = tempfile.NamedTemporaryFile(suffix=".fasta").name
         ds.consolidate(fa1)
         ds.write(out1)
         with ContigSet(out1) as ds_new:
             self.assertEqual(len([rec for rec in ds_new]), 1,
                              "failed on %d" % i)

# 需要导入模块: from pbcore.io import ContigSet [as 别名]
# 或者: from pbcore.io.ContigSet import consolidate [as 别名]
def __gather_contigset(resource_file_extension, input_files, output_file,
                       new_resource_file=None,
                       skip_empty=True):
    """
    :param input_files: List of file paths
    :param output_file: File Path
    :param new_resource_file: the path of the file to which the other contig
                              files are consolidated
    :param skip_empty: Ignore empty files (doesn't do much yet)

    :return: Output file

    :rtype: str
    """
    if skip_empty:
        _input_files = []
        for file_name in input_files:
            cs = ContigSet(file_name)
            if len(cs.toExternalFiles()) > 0:
                _input_files.append(file_name)
        input_files = _input_files
    tbr = ContigSet(*input_files)
    if not new_resource_file:
        if output_file.endswith('xml'):
            new_resource_file = output_file[:-3] + resource_file_extension
    tbr.consolidate(new_resource_file)
    tbr.newUuid()
    tbr.write(output_file)
    return output_file

# 需要导入模块: from pbcore.io import ContigSet [as 别名]
# 或者: from pbcore.io.ContigSet import consolidate [as 别名]
    def test_contigset_consolidate(self):
        #build set to merge
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")

        inFas = os.path.join(outdir, 'infile.fasta')
        outFas1 = os.path.join(outdir, 'tempfile1.fasta')
        outFas2 = os.path.join(outdir, 'tempfile2.fasta')

        # copy fasta reference to hide fai and ensure FastaReader is used
        backticks('cp {i} {o}'.format(
                      i=ReferenceSet(data.getXml(9)).toExternalFiles()[0],
                      o=inFas))
        rs1 = ContigSet(inFas)

        singletons = ['A.baumannii.1', 'A.odontolyticus.1']
        double = 'B.cereus.1'
        reader = rs1.resourceReaders()[0]
        exp_double = rs1.get_contig(double)
        exp_singles = [rs1.get_contig(name) for name in singletons]

        # todo: modify the names first:
        with FastaWriter(outFas1) as writer:
            writer.writeRecord(exp_singles[0])
            writer.writeRecord(exp_double.name + '_10_20', exp_double.sequence)
        with FastaWriter(outFas2) as writer:
            writer.writeRecord(exp_double.name + '_0_10',
                               exp_double.sequence + 'ATCGATCGATCG')
            writer.writeRecord(exp_singles[1])

        exp_double_seq = ''.join([exp_double.sequence,
                                  'ATCGATCGATCG',
                                  exp_double.sequence])
        exp_single_seqs = [rec.sequence for rec in exp_singles]

        acc_file = ContigSet(outFas1, outFas2)
        acc_file.induceIndices()
        log.debug(acc_file.toExternalFiles())
        self.assertEqual(len(acc_file), 4)
        self.assertEqual(len(list(acc_file)), 4)
        acc_file.consolidate()
        log.debug(acc_file.toExternalFiles())

        # open acc and compare to exp
        for name, seq in zip(singletons, exp_single_seqs):
            self.assertEqual(acc_file.get_contig(name).sequence[:], seq)
        self.assertEqual(acc_file.get_contig(double).sequence[:],
                         exp_double_seq)

        self.assertEqual(len(acc_file._openReaders), 1)
        self.assertEqual(len(acc_file.index), 3)
        self.assertEqual(len(acc_file._indexMap), 3)
        self.assertEqual(len(acc_file), 3)
        self.assertEqual(len(list(acc_file)), 3)

        # test merge:
        acc1 = ContigSet(outFas1)
        acc2 = ContigSet(outFas2)
        acc3 = acc1 + acc2

# 需要导入模块: from pbcore.io import ContigSet [as 别名]
# 或者: from pbcore.io.ContigSet import consolidate [as 别名]
def gather_contigset(input_files, output_file, new_resource_file=None,
                     skip_empty=True):
    """
    :param input_files: List of file paths
    :param output_file: File Path
    :param new_resource_file: the path of the file to which the other contig
                              files are consolidated
    :param skip_empty: Ignore empty files (doesn't do much yet)

    :return: Output file

    :rtype: str
    """
    tbr = ContigSet(*input_files)
    if not new_resource_file:
        if output_file.endswith('xml'):
            new_resource_file = output_file[:-3] + 'fasta'
    tbr.consolidate(new_resource_file)
    tbr.write(output_file)
    return output_file

# 需要导入模块: from pbcore.io import ContigSet [as 别名]
# 或者: from pbcore.io.ContigSet import consolidate [as 别名]
 def test_fastq_consolidate(self):
     fn = ('/pbi/dept/secondary/siv/testdata/SA3-RS/'
           'lambda/2590980/0008/Analysis_Results/'
           'm141115_075238_ethan_c100699872550000001'
           '823139203261572_s1_p0.1.subreads.fastq')
     fq_out = tempfile.NamedTemporaryFile(suffix=".fastq").name
     cfq_out = tempfile.NamedTemporaryFile(suffix=".fastq").name
     with open(fq_out, 'w') as fqh:
         with open(fn, 'r') as fih:
             for line in itertools.islice(fih, 240):
                 fqh.write(line)
     cset = ContigSet(fq_out)
     cset_l = sum(1 for _ in cset)
     self.assertEqual(cset_l, 60)
     cset.filters.addRequirement(length=[('>', 1000)])
     cset_l = sum(1 for _ in cset)
     self.assertEqual(cset_l, 23)
     cset.consolidate(cfq_out)
     cset_l = sum(1 for _ in cset)
     cfq = FastqReader(cfq_out)
     self.assertEqual(cset_l, 23)
     self.assertEqual(cset_l, sum(1 for _ in cfq))

# 需要导入模块: from pbcore.io import ContigSet [as 别名]
# 或者: from pbcore.io.ContigSet import consolidate [as 别名]
    def test_empty_fastq_consolidate(self):
        fn = ('/pbi/dept/secondary/siv/testdata/SA3-RS/'
              'lambda/2590980/0008/Analysis_Results/'
              'm141115_075238_ethan_c100699872550000001'
              '823139203261572_s1_p0.1.subreads.fastq')
        fq1_out = tempfile.NamedTemporaryFile(suffix="1.fastq").name
        fq2_out = tempfile.NamedTemporaryFile(suffix="2.fastq").name
        cfq_out = tempfile.NamedTemporaryFile(suffix=".fastq").name

        # Two full
        with open(fq1_out, 'w') as fqh:
            with open(fn, 'r') as fih:
                for line in itertools.islice(fih, 240):
                    fqh.write(line)
        with open(fq2_out, 'w') as fqh:
            with open(fn, 'r') as fih:
                for line in itertools.islice(fih, 240, 480):
                    fqh.write(line)
        cset = ContigSet(fq1_out, fq2_out)
        cset_l = sum(1 for _ in cset)
        self.assertEqual(cset_l, 120)
        cset.consolidate(cfq_out)
        cset_l = sum(1 for _ in cset)
        cfq = FastqReader(cfq_out)
        self.assertEqual(cset_l, 120)
        self.assertEqual(cset_l, sum(1 for _ in cfq))

        # one full one empty
        with open(fq1_out, 'w') as fqh:
            with open(fn, 'r') as fih:
                for line in itertools.islice(fih, 240):
                    fqh.write(line)
        with open(fq2_out, 'w') as fqh:
            with open(fn, 'r') as fih:
                fqh.write("")
        cset = ContigSet(fq1_out, fq2_out)
        cset_l = sum(1 for _ in cset)
        self.assertEqual(cset_l, 60)
        cset.consolidate(cfq_out)
        cset_l = sum(1 for _ in cset)
        cfq = FastqReader(cfq_out)
        self.assertEqual(cset_l, 60)
        self.assertEqual(cset_l, sum(1 for _ in cfq))

        # one empty one full
        with open(fq1_out, 'w') as fqh:
            with open(fn, 'r') as fih:
                fqh.write("")
        with open(fq2_out, 'w') as fqh:
            with open(fn, 'r') as fih:
                for line in itertools.islice(fih, 240):
                    fqh.write(line)
        cset = ContigSet(fq1_out, fq2_out)
        cset_l = sum(1 for _ in cset)
        self.assertEqual(cset_l, 60)
        cset.consolidate(cfq_out)
        cset_l = sum(1 for _ in cset)
        cfq = FastqReader(cfq_out)
        self.assertEqual(cset_l, 60)
        self.assertEqual(cset_l, sum(1 for _ in cfq))

        # both empty
        with open(fq1_out, 'w') as fqh:
            with open(fn, 'r') as fih:
                fqh.write("")
        with open(fq2_out, 'w') as fqh:
            with open(fn, 'r') as fih:
                fqh.write("")
        cset = ContigSet(fq1_out, fq2_out)
        cset_l = sum(1 for _ in cset)
        self.assertEqual(cset_l, 0)
        cset.consolidate(cfq_out)
        cset_l = sum(1 for _ in cset)
        cfq = FastqReader(cfq_out)
        self.assertEqual(cset_l, 0)
        self.assertEqual(cset_l, sum(1 for _ in cfq))

# 需要导入模块: from pbcore.io import ContigSet [as 别名]
# 或者: from pbcore.io.ContigSet import consolidate [as 别名]
def consolidateXml(args):
    """Combine BAMs and apply the filters described in the XML file, producing
    one consolidated XML"""
    dset = ContigSet(args.infile)
    dset.consolidate(args.datafile)
    dset.write(args.xmlfile)