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 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)
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 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 _trna_annotation(data):
"""
use tDRmapper to quantify tRNAs
"""
mirbase = op.abspath(op.dirname(dd.get_mirbase_ref(data)))
trna_ref = op.join(mirbase, "trna_mature_pre.fa")
name = dd.get_sample_name(data)
work_dir = utils.safe_makedir(
os.path.join(dd.get_work_dir(data), "trna", name))
in_file = op.basename(data["clean_fastq"])
tdrmapper = os.path.join(os.path.dirname(sys.executable),
"TdrMappingScripts.pl")
if not file_exists(trna_ref) or not file_exists(tdrmapper):
logger.info("There is no tRNA annotation to run TdrMapper.")
return None
out_file = op.join(work_dir, in_file + ".hq_cs.mapped")
if not file_exists(out_file):
with tx_tmpdir(data) as txdir:
with utils.chdir(txdir):
utils.symlink_plus(data["clean_fastq"],
op.join(txdir, in_file))
cmd = ("perl {tdrmapper} {trna_ref} {in_file}").format(
**locals())
do.run(cmd, "tRNA for %s" % name)
for filename in glob.glob("*mapped*"):
shutil.move(filename, work_dir)
return out_file
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 _trna_annotation(data):
"""
use tDRmapper to quantify tRNAs
"""
mirbase = op.abspath(op.dirname(dd.get_mirbase_ref(data)))
trna_ref = op.join(mirbase, "trna_mature_pre.fa")
name = dd.get_sample_name(data)
work_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "trna", name))
in_file = op.basename(data["clean_fastq"])
tdrmapper = os.path.join(os.path.dirname(sys.executable), "TdrMappingScripts.pl")
if not file_exists(trna_ref) or not file_exists(tdrmapper):
logger.info("There is no tRNA annotation to run TdrMapper.")
return None
out_file = op.join(work_dir, in_file + ".hq_cs.mapped")
if not file_exists(out_file):
with tx_tmpdir(data) as txdir:
with utils.chdir(txdir):
utils.symlink_plus(data["clean_fastq"], op.join(txdir, in_file))
cmd = ("perl {tdrmapper} {trna_ref} {in_file}").format(**locals())
do.run(cmd, "tRNA for %s" % name)
for filename in glob.glob("*mapped*"):
shutil.move(filename, work_dir)
return out_file
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)
