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)
}
def to_i(i):
return "chunk-id-{i}".format(i=i)
def to_p(i):
return PipelineChunk(to_i(i), **f(i))
nchunks = 5
pipeline_chunks = [to_p(i) for i in range(nchunks)]
log.debug(pipeline_chunks)
tmp_dir = get_temp_dir("pipeline-chunks")
tmp_name = get_temp_file("_chunk.json", tmp_dir)
write_pipeline_chunks(pipeline_chunks, tmp_name, "Example chunk file")
pchunks = load_pipeline_chunks_from_json(tmp_name)
assert len(pchunks) == nchunks
def __args_gather_runner(func, chunk_json, output_file, chunk_key):
chunks = load_pipeline_chunks_from_json(chunk_json)
# Allow looseness
if not chunk_key.startswith('$chunk.'):
chunk_key = '$chunk.' + chunk_key
log.warn("Prepending chunk key with '$chunk.' to '{c}'".format(c=chunk_key))
fastx_files = _get_datum_from_chunks_by_chunk_key(chunks, chunk_key)
_ = func(fastx_files, output_file)
return 0
def run_main(chunk_json, fasta_output, chunk_key):
chunks = load_pipeline_chunks_from_json(chunk_json)
# Allow looseness
if not chunk_key.startswith('$chunk.'):
chunk_key = '$chunk.' + chunk_key
log.warn("Prepending chunk key with '$chunk.' to '{c}'".format(c=chunk_key))
fastx_files = get_datum_from_chunks_by_chunk_key(chunks, chunk_key)
_ = gather_fasta(fastx_files, fasta_output)
return 0
def __args_gather_runner(func, chunk_json, output_file, chunk_key):
chunks = load_pipeline_chunks_from_json(chunk_json)
# Allow looseness
if not chunk_key.startswith("$chunk."):
chunk_key = "$chunk." + chunk_key
log.warn("Prepending chunk key with '$chunk.' to '{c}'".format(c=chunk_key))
else:
chunk_key = chunk_key
fastx_files = _get_datum_from_chunks_by_chunk_key(chunks, chunk_key)
_ = func(fastx_files, output_file)
return 0
def run_main(chunk_json, fasta_output, chunk_key):
chunks = load_pipeline_chunks_from_json(chunk_json)
# Allow looseness
if not chunk_key.startswith('$chunk.'):
chunk_key = '$chunk.' + chunk_key
log.warn(
"Prepending chunk key with '$chunk.' to '{c}'".format(c=chunk_key))
fastx_files = get_datum_from_chunks_by_chunk_key(chunks, chunk_key)
_ = gather_fasta(fastx_files, fasta_output)
return 0
def run_main(chunk_json, fofn_output, chunk_key):
with cd(os.path.dirname(fofn_output)):
chunks = load_pipeline_chunks_from_json(chunk_json)
# Allow looseness
if not chunk_key.startswith('$chunk.'):
chunk_key = '$chunk.' + chunk_key
log.warn("Prepending chunk key with '$chunk.' to '{c}'".format(c=chunk_key))
fofn_files = get_datum_from_chunks_by_chunk_key(chunks, chunk_key)
print("fofn_files:%s %s" %(repr(fofn_files), repr(fofn_output)))
# Combine all into one.
with open(fofn_output, 'w') as ofs:
for fn in fofn_files:
with open(fn) as ifs:
ofs.write(ifs.read())
def run_main(chunk_json, fofn_output, chunk_key):
with cd(os.path.dirname(fofn_output)):
chunks = load_pipeline_chunks_from_json(chunk_json)
# Allow looseness
if not chunk_key.startswith('$chunk.'):
chunk_key = '$chunk.' + chunk_key
log.warn("Prepending chunk key with '$chunk.' to '{c}'".format(c=chunk_key))
fofn_files = get_datum_from_chunks_by_chunk_key(chunks, chunk_key)
print("fofn_files:%s %s" %(repr(fofn_files), repr(fofn_output)))
# Combine all into one.
with open(fofn_output, 'w') as ofs:
for fn in fofn_files:
with open(fn) as ifs:
ofs.write(ifs.read())
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_dir = get_temp_dir("pipeline-chunks")
tmp_name = get_temp_file("_chunk.json", tmp_dir)
write_pipeline_chunks(pipeline_chunks, tmp_name, "Example chunk file")
pchunks = load_pipeline_chunks_from_json(tmp_name)
self.assertEquals(len(pchunks), nchunks)
