def run(data): config = data[0][0]['config'] work_dir = dd.get_work_dir(data[0][0]) genome = dd.get_ref_file(data[0][0]) mirdeep2 = os.path.join(os.path.dirname(sys.executable), "miRDeep2.pl") perl_exports = get_perl_exports() hairpin, mature, species = "none", "none", "na" rfam_file = dd.get_mirdeep2_file(data[0][0]) if file_exists(dd.get_mirbase_hairpin(data[0][0])): species = dd.get_species(data[0][0]) hairpin = dd.get_mirbase_hairpin(data[0][0]) mature = dd.get_mirbase_mature(data[0][0]) logger.debug("Preparing for mirdeep2 analysis.") bam_file = op.join(work_dir, "align", "seqs.bam") seqs_dir = op.join(work_dir, "seqcluster", "prepare") collapsed = op.join(seqs_dir, "seqs.ma") out_dir = op.join(work_dir, "mirdeep2") out_file = op.join(out_dir, "result_res.csv") safe_makedir(out_dir) with chdir(out_dir): collapsed, bam_file = _prepare_inputs(collapsed, bam_file, out_dir) cmd = ("{perl_exports} && perl {mirdeep2} {collapsed} {genome} {bam_file} {mature} none {hairpin} -f {rfam_file} -r simple -c -P -t {species} -z res").format(**locals()) if file_exists(mirdeep2) and not file_exists(out_file) and file_exists(rfam_file): do.run(cmd.format(**locals()), "Running mirdeep2.") if file_exists(out_file): novel_db = _parse_novel(out_file, dd.get_species(data[0][0])) return novel_db
def run(data): config = data[0][0]['config'] work_dir = dd.get_work_dir(data[0][0]) genome = dd.get_ref_file(data[0][0]) mirdeep2 = os.path.join(os.path.dirname(sys.executable), "miRDeep2.pl") perl_exports = get_perl_exports() hairpin, mature, species = "none", "none", "na" rfam_file = dd.get_mirdeep2_file(data[0][0]) if file_exists(dd.get_mirbase_hairpin(data[0][0])): species = dd.get_species(data[0][0]) hairpin = dd.get_mirbase_hairpin(data[0][0]) mature = dd.get_mirbase_mature(data[0][0]) bam_file = op.join(work_dir, "align", "seqs.bam") seqs_dir = op.join(work_dir, "seqcluster", "prepare") collapsed = op.join(seqs_dir, "seqs.ma") out_dir = op.join(work_dir, "mirdeep2") out_file = op.join(out_dir, "result_res.csv") safe_makedir(out_dir) with chdir(out_dir): collapsed, bam_file = _prepare_inputs(collapsed, bam_file, out_dir) cmd = ("{perl_exports} && perl {mirdeep2} {collapsed} {genome} {bam_file} {mature} none {hairpin} -f {rfam_file} -r simple -c -d -P -t {species} -z res").format(**locals()) if file_exists(mirdeep2) and not file_exists(out_file) and file_exists(rfam_file): do.run(cmd.format(**locals()), "Running mirdeep2.") if file_exists(out_file): novel_db = _parse_novel(out_file, dd.get_species(data[0][0])) return novel_db
def run(data): config = data[0][0]['config'] work_dir = dd.get_work_dir(data[0][0]) genome = dd.get_ref_file(data[0][0]) mirdeep2 = os.path.join(os.path.dirname(sys.executable), "miRDeep2.pl") perl_exports = get_perl_exports() hairpin, mature, species = "none", "none", "na" rfam_file = dd.get_mirdeep2_file(data[0][0]) if file_exists(dd.get_mirbase_hairpin(data[0][0])): species = dd.get_species(data[0][0]) hairpin = dd.get_mirbase_hairpin(data[0][0]) mature = dd.get_mirbase_mature(data[0][0]) logger.debug("Preparing for mirdeep2 analysis.") bam_file = op.join(work_dir, "align", "seqs.bam") seqs_dir = op.join(work_dir, "seqcluster", "prepare") collapsed = op.join(seqs_dir, "seqs.ma") out_dir = op.join(work_dir, "mirdeep2") out_file = op.join(out_dir, "result_res.csv") safe_makedir(out_dir) if not file_exists(rfam_file): logger.warning("mirdeep2 Rfam file not instaled. Skipping...") return None if not file_exists(mirdeep2): logger.warning("mirdeep2 executable file not found. Skipping...") return None with chdir(out_dir): collapsed, bam_file = _prepare_inputs(collapsed, bam_file, out_dir) cmd = ( "{perl_exports} && perl {mirdeep2} {collapsed} {genome} {bam_file} {mature} none {hairpin} -f {rfam_file} -r simple -c -P -t {species} -z res" ).format(**locals()) if not file_exists(out_file): try: do.run(cmd.format(**locals()), "Running mirdeep2.") except: logger.warning( "mirdeep2 failed. Please report the error to https://github.com/lpantano/mirdeep2_core/issues." ) if file_exists(out_file): novel_db = _parse_novel(out_file, dd.get_species(data[0][0])) return novel_db
def run(data): config = data[0][0]['config'] work_dir = dd.get_work_dir(data[0][0]) genome = dd.get_ref_file(data[0][0]) mirdeep2 = os.path.join(os.path.dirname(sys.executable), "miRDeep2.pl") perl_exports = get_perl_exports() hairpin, mature, species = "none", "none", "na" rfam_file = dd.get_mirdeep2_file(data[0][0]) if file_exists(dd.get_mirbase_hairpin(data[0][0])): species = dd.get_species(data[0][0]) hairpin = dd.get_mirbase_hairpin(data[0][0]) mature = dd.get_mirbase_mature(data[0][0]) logger.debug("Preparing for mirdeep2 analysis.") bam_file = op.join(work_dir, "align", "seqs.bam") seqs_dir = op.join(work_dir, "seqcluster", "prepare") collapsed = op.join(seqs_dir, "seqs.ma") out_dir = op.join(work_dir, "mirdeep2") out_file = op.join(out_dir, "result_res.csv") safe_makedir(out_dir) if not file_exists(rfam_file): logger.warning("mirdeep2 Rfam file not instaled. Skipping...") return None if not file_exists(mirdeep2): logger.warning("mirdeep2 executable file not found. Skipping...") return None with chdir(out_dir): collapsed, bam_file = _prepare_inputs(collapsed, bam_file, out_dir) cmd = ("{perl_exports} && perl {mirdeep2} {collapsed} {genome} {bam_file} {mature} none {hairpin} -f {rfam_file} -r simple -c -P -t {species} -z res").format(**locals()) if not file_exists(out_file): try: do.run(cmd.format(**locals()), "Running mirdeep2.") except: logger.warning("mirdeep2 failed. Please report the error to https://github.com/lpantano/mirdeep2_core/issues.") if file_exists(out_file): novel_db = _parse_novel(out_file, dd.get_species(data[0][0])) return novel_db