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