def assemble_transcripts(align_file, ref_file, config):
"""Create transcript assemblies using Cufflinks.
"""
work_dir, fname = os.path.split(align_file)
cores = config.get("resources", {}).get("cufflinks", {}).get("cores", None)
core_flags = ["-p", str(cores)] if cores else []
out_dir = os.path.join(work_dir,
"{base}-cufflinks".format(base=os.path.splitext(fname)[0]))
cl = [config_utils.get_program("cufflinks", config),
align_file,
"-o", out_dir,
"-b", ref_file,
"-u"]
cl += core_flags
tx_file = configured_ref_file("transcripts", config, ref_file)
tx_mask_file = configured_ref_file("transcripts_mask", config, ref_file)
if tx_file:
cl += ["-g", tx_file]
if tx_mask_file:
cl += ["-M", tx_mask_file]
out_tx_file = os.path.join(out_dir, "transcripts.gtf")
if not os.path.exists(out_tx_file):
subprocess.check_call(cl)
assert os.path.exists(out_tx_file)
return out_tx_file
def assemble_transcripts(align_file, ref_file, config):
"""Create transcript assemblies using Cufflinks.
"""
work_dir, fname = os.path.split(align_file)
cores = config.get("resources", {}).get("cufflinks", {}).get("cores", None)
core_flags = ["-p", str(cores)] if cores else []
out_dir = os.path.join(
work_dir, "{base}-cufflinks".format(base=os.path.splitext(fname)[0]))
cl = [
config["program"].get("cufflinks", "cufflinks"), align_file, "-o",
out_dir, "-b", ref_file, "-u"
]
cl += core_flags
tx_file = configured_ref_file("transcripts", config, ref_file)
tx_mask_file = configured_ref_file("transcripts_mask", config, ref_file)
if tx_file:
cl += ["-g", tx_file]
if tx_mask_file:
cl += ["-M", tx_mask_file]
out_tx_file = os.path.join(out_dir, "transcripts.gtf")
if not os.path.exists(out_tx_file):
subprocess.check_call(cl)
assert os.path.exists(out_tx_file)
return out_tx_file
def assemble_transcripts(align_file, ref_file, config):
"""Create transcript assemblies using Cufflinks.
"""
work_dir, fname = os.path.split(align_file)
out_dir = os.path.join(work_dir,
"{base}-cufflinks".format(base=os.path.splitext(fname)[0]))
cl = [config["program"].get("cufflinks", "cufflinks"),
align_file,
"-o", out_dir,
"-b", ref_file,
"-u"]
tx_file = configured_ref_file("transcripts", config, ref_file)
tx_mask_file = configured_ref_file("transcripts_mask", config, ref_file)
if tx_file:
cl += ["-g", tx_file]
if tx_mask_file:
cl += ["-M", tx_mask_file]
out_tx_file = os.path.join(out_dir, "transcripts.gtf")
if not os.path.exists(out_tx_file):
subprocess.check_call(cl)
assert os.path.exists(out_tx_file)
return out_tx_file
