Example #1
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
Example #2
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())