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):
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 sample_annotation(data):
"""
Annotate miRNAs using miRBase database with seqbuster tool
"""
names = data["rgnames"]['sample']
tools = dd.get_expression_caller(data)
work_dir = os.path.join(dd.get_work_dir(data), "mirbase")
out_dir = os.path.join(work_dir, names)
utils.safe_makedir(out_dir)
out_file = op.join(out_dir, names)
if dd.get_mirbase_hairpin(data):
mirbase = op.abspath(op.dirname(dd.get_mirbase_hairpin(data)))
data['seqbuster'] = _miraligner(data["collapse"], out_file,
dd.get_species(data), mirbase,
data['config'])
else:
logger.debug("No annotation file from miRBase.")
sps = dd.get_species(data) if dd.get_species(data) else "None"
logger.debug("Looking for mirdeep2 database for %s" % names)
if file_exists(
op.join(dd.get_work_dir(data), "mirdeep2", "novel", "hairpin.fa")):
data['seqbuster_novel'] = _miraligner(
data["collapse"], "%s_novel" % out_file, sps,
op.join(dd.get_work_dir(data), "mirdeep2", "novel"),
data['config'])
if "trna" in tools:
data['trna'] = _trna_annotation(data)
data = spikein.counts_spikein(data)
return [[data]]
def sample_annotation(data):
"""
Annotate miRNAs using miRBase database with seqbuster tool
"""
names = data["rgnames"]['sample']
tools = dd.get_expression_caller(data)
work_dir = os.path.join(dd.get_work_dir(data), "mirbase")
out_dir = os.path.join(work_dir, names)
utils.safe_makedir(out_dir)
out_file = op.join(out_dir, names)
if dd.get_mirbase_hairpin(data):
mirbase = op.abspath(op.dirname(dd.get_mirbase_hairpin(data)))
if utils.file_exists(data["collapse"]):
data['transcriptome_bam'] = _align(data["collapse"], dd.get_mirbase_hairpin(data), out_file, data)
data['seqbuster'] = _miraligner(data["collapse"], out_file, dd.get_species(data), mirbase, data['config'])
else:
logger.debug("Trimmed collapsed file is empty for %s." % names)
else:
logger.debug("No annotation file from miRBase.")
sps = dd.get_species(data) if dd.get_species(data) else "None"
logger.debug("Looking for mirdeep2 database for %s" % names)
if file_exists(op.join(dd.get_work_dir(data), "mirdeep2", "novel", "hairpin.fa")):
data['seqbuster_novel'] = _miraligner(data["collapse"], "%s_novel" % out_file, sps, op.join(dd.get_work_dir(data), "mirdeep2", "novel"), data['config'])
if "trna" in tools:
data['trna'] = _mint_trna_annotation(data)
data = spikein.counts_spikein(data)
return [[data]]
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()
mirbase = op.abspath(op.dirname(dd.get_mirbase_ref(data[0][0])))
species = dd.get_species(data[0][0])
hairpin = op.join(mirbase, "hairpin.fa")
mature = op.join(mirbase, "mature.fa")
rfam_file = op.join(mirbase, "Rfam_for_miRDeep.fa")
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} && {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(mature) 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 sample_annotation(data):
"""
Annotate miRNAs using miRBase database with seqbuster tool
"""
names = data["rgnames"]['sample']
work_dir = os.path.join(dd.get_work_dir(data), "mirbase")
out_dir = os.path.join(work_dir, names)
utils.safe_makedir(out_dir)
out_file = op.join(out_dir, names)
if not dd.get_mirbase_ref(data):
raise ValueError(
"There is no smallRNA genome data."
"Please, run bcbio_nextgen.py upgrade -u skip --genome build_name."
)
mirbase = op.abspath(op.dirname(dd.get_mirbase_ref(data)))
data['seqbuster'] = _miraligner(data["collapse"], out_file,
dd.get_species(data), mirbase,
data['config'])
if file_exists(
op.join(dd.get_work_dir(data), "mirdeep2", "novel", "hairpin.fa")):
data['seqbuster_novel'] = _miraligner(
data["collapse"], "%s_novel" % out_file, dd.get_species(data),
op.join(dd.get_work_dir(data), "mirdeep2", "novel"),
data['config'])
data['trna'] = _trna_annotation(data)
return [[data]]
def sample_annotation(data):
"""
Annotate miRNAs using miRBase database with seqbuster tool
"""
names = data["rgnames"]['sample']
work_dir = os.path.join(dd.get_work_dir(data), "mirbase")
out_dir = os.path.join(work_dir, names)
utils.safe_makedir(out_dir)
out_file = op.join(out_dir, names)
if dd.get_mirbase_hairpin(data):
mirbase = op.abspath(op.dirname(dd.get_mirbase_hairpin(data)))
data['seqbuster'] = _miraligner(data["collapse"], out_file,
dd.get_species(data), mirbase,
data['config'])
sps = dd.get_species(data) if dd.get_species(data) else "None"
if file_exists(
op.join(dd.get_work_dir(data), "mirdeep2", "novel", "hairpin.fa")):
data['seqbuster_novel'] = _miraligner(
data["collapse"], "%s_novel" % out_file, sps,
op.join(dd.get_work_dir(data), "mirdeep2", "novel"),
data['config'])
data['trna'] = _trna_annotation(data)
return [[data]]
def run(data):
"""Proxy function to run the tool"""
sample = data[0][0]
work_dir = dd.get_work_dir(sample)
out_dir = os.path.join(work_dir, "mirge")
lib = _find_lib(sample)
mirge = _find_mirge(sample)
bowtie = _find_bowtie(sample)
sps = dd.get_species(sample)
species = SPS.get(sps, "")
if not species:
raise ValueError(
"species not supported (hsa, mmu, rno, dre, cel, dme): %s" % sps)
if not lib:
raise ValueError(
"-lib option is not set up in resources for mirge tool."
" Read above warnings lines.")
if not utils.file_exists(out_dir):
with tx_tmpdir() as tmp_dir:
sample_file = _create_sample_file(data, tmp_dir)
do.run(_cmd().format(**locals()), "Running miRge2.0.")
shutil.move(tmp_dir, out_dir)
return [
os.path.abspath(fn)
for fn in glob.glob(os.path.join(out_dir, "*", "*"))
]
def sample_annotation(data):
"""
Annotate miRNAs using miRBase database with seqbuster tool
"""
names = data["rgnames"]['sample']
work_dir = os.path.join(dd.get_work_dir(data), "mirbase")
out_dir = os.path.join(work_dir, names)
utils.safe_makedir(out_dir)
out_file = op.join(out_dir, names)
if dd.get_mirbase_hairpin(data):
mirbase = op.abspath(op.dirname(dd.get_mirbase_hairpin(data)))
data['seqbuster'] = _miraligner(data["collapse"], out_file, dd.get_species(data), mirbase, data['config'])
sps = dd.get_species(data) if dd.get_species(data) else "None"
if file_exists(op.join(dd.get_work_dir(data), "mirdeep2", "novel", "hairpin.fa")):
data['seqbuster_novel'] = _miraligner(data["collapse"], "%s_novel" % out_file, sps, op.join(dd.get_work_dir(data), "mirdeep2", "novel"), data['config'])
data['trna'] = _trna_annotation(data)
return [[data]]
def mirbase(data):
names = data["rgnames"]['sample']
work_dir = os.path.join(dd.get_work_dir(data), "mirbase")
out_dir = os.path.join(work_dir, names)
utils.safe_makedir(out_dir)
out_file = op.join(out_dir, names)
mirbase = op.abspath(op.dirname(dd.get_mirbase_ref(data)))
mirbase = op.abspath(op.dirname(dd.get_mirbase_ref(data)))
data['seqbuster'] = _miraligner(data["collapse"], out_file, dd.get_species(data), mirbase, data['config'])
return [[data]]
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 mirbase(data):
names = data["rgnames"]['sample']
work_dir = os.path.join(dd.get_work_dir(data), "mirbase")
out_dir = os.path.join(work_dir, names)
utils.safe_makedir(out_dir)
out_file = op.join(out_dir, names)
mirbase = op.abspath(op.dirname(dd.get_mirbase_ref(data)))
mirbase = op.abspath(op.dirname(dd.get_mirbase_ref(data)))
data['seqbuster'] = _miraligner(data["collapse"], out_file,
dd.get_species(data), mirbase,
data['config'])
return [[data]]
def mirbase(data):
names = data["rgnames"]['sample']
work_dir = os.path.join(dd.get_work_dir(data), "mirbase")
out_dir = os.path.join(work_dir, names)
utils.safe_makedir(out_dir)
out_file = op.join(out_dir, names)
if not dd.get_mirbase_ref(data):
raise ValueError("There is no smallRNA genome data."
"Please, run bcbio_nextgen.py upgrade -u skip --genome build_name.")
mirbase = op.abspath(op.dirname(dd.get_mirbase_ref(data)))
mirbase = op.abspath(op.dirname(dd.get_mirbase_ref(data)))
data['seqbuster'] = _miraligner(data["collapse"], out_file, dd.get_species(data), mirbase, data['config'])
return [[data]]
def mirbase(data):
names = data["rgnames"]['sample']
work_dir = os.path.join(dd.get_work_dir(data), "mirbase")
out_dir = os.path.join(work_dir, names)
utils.safe_makedir(out_dir)
out_file = op.join(out_dir, names)
if not dd.get_mirbase_ref(data):
raise ValueError(
"There is no smallRNA genome data."
"Please, run bcbio_nextgen.py upgrade -u skip --genome build_name."
)
mirbase = op.abspath(op.dirname(dd.get_mirbase_ref(data)))
mirbase = op.abspath(op.dirname(dd.get_mirbase_ref(data)))
data['seqbuster'] = _miraligner(data["collapse"], out_file,
dd.get_species(data), mirbase,
data['config'])
return [[data]]
def sample_annotation(data):
"""
Annotate miRNAs using miRBase database with seqbuster tool
"""
names = data["rgnames"]['sample']
work_dir = os.path.join(dd.get_work_dir(data), "mirbase")
out_dir = os.path.join(work_dir, names)
utils.safe_makedir(out_dir)
out_file = op.join(out_dir, names)
if not dd.get_mirbase_ref(data):
raise ValueError("There is no smallRNA genome data."
"Please, run bcbio_nextgen.py upgrade -u skip --genome build_name.")
mirbase = op.abspath(op.dirname(dd.get_mirbase_ref(data)))
data['seqbuster'] = _miraligner(data["collapse"], out_file, dd.get_species(data), mirbase, data['config'])
if file_exists(op.join(dd.get_work_dir(data), "mirdeep2", "novel", "hairpin.fa")):
data['seqbuster_novel'] = _miraligner(data["collapse"], "%s_novel" % out_file, dd.get_species(data), op.join(dd.get_work_dir(data), "mirdeep2", "novel"), data['config'])
data['trna'] = _trna_annotation(data)
return [[data]]
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 = config_utils.get_program("miRDeep2.pl", config)
mirbase = op.abspath(op.dirname(dd.get_mirbase_ref(data[0][0])))
species = dd.get_species(data[0][0])
hairpin = op.join(mirbase, "hairpin.fa")
mature = op.join(mirbase, "mature.fa")
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 = ("{mirdeep2} {collapsed} {genome} {bam_file} {mature} none {hairpin} -r simple -c -d -P -t {species} -z res").format(**locals())
if mirdeep2 and not file_exists(out_file) and file_exists(mature):
do.run(cmd.format(**locals()), "Running mirdeep2.")
_parse_novel(out_file)
def run(data):
"""Proxy function to run the tool"""
sample = data[0][0]
work_dir = dd.get_work_dir(sample)
out_dir = os.path.join(work_dir, "mirge")
lib = _find_lib(sample)
mirge = _find_mirge(sample)
bowtie = _find_bowtie(sample)
sps = dd.get_species(sample)
species = SPS.get(sps, "")
if not species:
raise ValueError("species not supported (hsa, mmu, rno, dre, cel, dme): %s" % sps)
if not lib:
raise ValueError("-lib option is not set up in resources for mirge tool."
" Read above warnings lines.")
if not utils.file_exists(out_dir):
with tx_tmpdir() as tmp_dir:
sample_file = _create_sample_file(data, tmp_dir)
do.run(_cmd().format(**locals()), "Running miRge2.0.")
shutil.move(tmp_dir, out_dir)
return [os.path.abspath(fn) for fn in glob.glob(os.path.join(out_dir, "*", "*"))]
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 = config_utils.get_program("miRDeep2.pl", config)
mirbase = op.abspath(op.dirname(dd.get_mirbase_ref(data[0][0])))
species = dd.get_species(data[0][0])
hairpin = op.join(mirbase, "hairpin.fa")
mature = op.join(mirbase, "mature.fa")
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 = (
"{mirdeep2} {collapsed} {genome} {bam_file} {mature} none {hairpin} -r simple -c -d -P -t {species} -z res"
).format(**locals())
if mirdeep2 and not file_exists(out_file) and file_exists(mature):
do.run(cmd.format(**locals()), "Running mirdeep2.")
_parse_novel(out_file)