Python ContigSet.toExternalFiles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 toExternalFiles [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 toExternalFiles [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 toExternalFiles [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 toExternalFiles [as 别名]
def _get_fasta_path(file_name):
    if file_name.endswith(".contigset.xml"):
        ds = ContigSet(file_name)
        fasta_files = ds.toExternalFiles()
        assert len(fasta_files) == 1
        return fasta_files[0]
    return file_name