Python load_pipeline_chunks_from_jsonの例

コード例 #1

ファイル: gather.py プロジェクト: yqin22/pbsmrtpipe

def __gather_runner(func, chunk_input_json, output_file, chunk_key):
    chunks = IO.load_pipeline_chunks_from_json(chunk_input_json)

    # Allow looseness
    if not chunk_key.startswith('$chunk.'):
        chunk_key = '$chunk.' + chunk_key
        log.warn("Prepending chunk key with '$chunk.' to '{c}'".format(c=chunk_key))

    chunked_files = get_datum_from_chunks_by_chunk_key(chunks, chunk_key)
    _ = func(chunked_files, output_file)
    return 0

コード例 #2

def __gather_runner(func, chunk_input_json, output_file, chunk_key, **kwargs):
    chunks = IO.load_pipeline_chunks_from_json(chunk_input_json)

    # Allow looseness
    if not chunk_key.startswith('$chunk.'):
        chunk_key = '$chunk.' + chunk_key
        log.warn("Prepending chunk key with '$chunk.' to '{c}'".format(c=chunk_key))

    chunked_files = get_datum_from_chunks_by_chunk_key(chunks, chunk_key)
    _ = func(chunked_files, output_file, **kwargs)
    return 0

コード例 #3

ファイル: test_pb_io.py プロジェクト: pombredanne/pbsmrtpipe

    def test_write_chunks(self):

        def f(i):
            return {"{c}movie_fofn_id".format(c=PipelineChunk.CHUNK_KEY_PREFIX): "/path/to_movie-{i}.fofn".format(i=i),
                    "{c}region_fofn_id".format(c=PipelineChunk.CHUNK_KEY_PREFIX): "/path/rgn_{i}.fofn".format(i=i)}

        to_i = lambda i: "chunk-id-{i}".format(i=i)
        to_p = lambda i: PipelineChunk(to_i(i), **f(i))

        nchunks = 5
        pipeline_chunks = [to_p(i) for i in xrange(nchunks)]
        log.debug(pipeline_chunks)
        tmp_name = get_temp_file("_chunk.json")

        IO.write_pipeline_chunks(pipeline_chunks, tmp_name, "Example chunk file")

        pchunks = IO.load_pipeline_chunks_from_json(tmp_name)
        self.assertEquals(len(pchunks), nchunks)

コード例 #4

ファイル: test_pb_io.py プロジェクト: yqin22/pbsmrtpipe

    def test_write_chunks(self):
        def f(i):
            return {
                "{c}movie_fofn_id".format(c=PipelineChunk.CHUNK_KEY_PREFIX):
                "/path/to_movie-{i}.fofn".format(i=i),
                "{c}region_fofn_id".format(c=PipelineChunk.CHUNK_KEY_PREFIX):
                "/path/rgn_{i}.fofn".format(i=i)
            }

        to_i = lambda i: "chunk-id-{i}".format(i=i)
        to_p = lambda i: PipelineChunk(to_i(i), **f(i))

        nchunks = 5
        pipeline_chunks = [to_p(i) for i in xrange(nchunks)]
        log.debug(pipeline_chunks)
        tmp_name = get_temp_file("_chunk.json")

        IO.write_pipeline_chunks(pipeline_chunks, tmp_name,
                                 "Example chunk file")

        pchunks = IO.load_pipeline_chunks_from_json(tmp_name)
        self.assertEquals(len(pchunks), nchunks)

コード例 #5

ファイル: gather.py プロジェクト: yqin22/pbsmrtpipe

def _validate_chunk_json_file(path):
    chunks = IO.load_pipeline_chunks_from_json(path)
    return path

コード例 #6

def _validate_chunk_json_file(path):
    chunks = IO.load_pipeline_chunks_from_json(path)
    return path