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