def ice_quiver_postprocess_a_cluster_bin(cluster_out_dir, ipq_opts):
"""
ice_quiver_postprocess a cluster bin, create summary.json,
cluster_report.csv, hq|lq_isoforms.fa|fq.
return hq.fq and lq.fq
Parameters:
cluster_out_dir - root dir running ICE, ice_partial and ice_quiver
for this cluster bin.
"""
_jobs_log = op.join(cluster_out_dir, "log", "submitted_quiver_jobs.txt")
shell_scripts = []
for file_name in os.listdir(op.join(cluster_out_dir, "quivered")):
if file_name.endswith(".sh"):
shell_scripts.append(file_name)
with open(_jobs_log, 'w') as f:
f.write("\n".join(["\t".join(["local", s]) for s in shell_scripts]))
icep = IceQuiverPostprocess(root_dir=cluster_out_dir,
ipq_opts=ipq_opts)
for file_name in os.listdir(op.join(cluster_out_dir, "quivered")):
if file_name.endswith(".sh"):
shell_scripts.append(file_name)
icep.run()
return (icep.quivered_good_fq, icep.quivered_bad_fq)
def run(self):
"""Run"""
iceq = IceQuiver(root_dir=self.root_dir, bas_fofn=self.bas_fofn,
fasta_fofn=self.fasta_fofn, sge_opts=self.sge_opts,
tmp_dir=self.tmp_dir)
iceq.validate_inputs()
iceq.run()
icepq = IceQuiverPostprocess(root_dir=self.root_dir,
use_sge=self.sge_opts.use_sge,
quit_if_not_done=False,
ipq_opts=self.ipq_opts)
icepq.run()
return 0
def run(self):
"""Run"""
iceq = IceQuiver(root_dir=self.root_dir,
bas_fofn=self.bas_fofn,
fasta_fofn=self.fasta_fofn,
sge_opts=self.sge_opts,
tmp_dir=self.tmp_dir)
iceq.validate_inputs()
iceq.run()
icepq = IceQuiverPostprocess(root_dir=self.root_dir,
use_sge=self.sge_opts.use_sge,
quit_if_not_done=False,
ipq_opts=self.ipq_opts)
icepq.run()
return 0
class Polish(IceFiles):
"""Polish isoforms clusters using Quiver."""
def __init__(self,
root_dir,
nfl_fa,
bas_fofn,
ccs_fofn,
ice_opts,
sge_opts,
ipq_opts,
fasta_fofn=None,
tmp_dir=None):
"""
root_dir --- IceFiles.root_dir, usually data/clusterOutDir
nfl_fa --- non-full-length reads in fasta, e.g., isoseq_nfl.fasta
bas_fofn --- e.g. input.fofn of bas|bax.h5 files
ccs_fofn --- e.g. ccs.fofn of ccs files.
ipq_opts --- IceQuiverHQLQOptions
qv_trim_5: ignore QV of n bases in the 5' end
qv_trim_3: ignore QV of n bases in the 3' end
hq_quiver_min_accuracy: minimum allowed quiver accuracy
to mark an isoform as high quality
hq_isoforms_fa|fq: polished, hiqh quality consensus
isoforms in fasta|q
lq_isoforms_fa|fq: polished, low quality consensus
isoforms in fasta|q
"""
IceFiles.__init__(self,
prog_name="IcePolish",
root_dir=root_dir,
bas_fofn=bas_fofn,
ccs_fofn=ccs_fofn,
fasta_fofn=fasta_fofn,
tmp_dir=tmp_dir)
self.nfl_fa = realpath(nfl_fa)
self.ice_opts = ice_opts
self.sge_opts = sge_opts
self.ipq_opts = ipq_opts
self.add_log("ece_penalty: {0}, ece_min_len: {1}".format(
self.ice_opts.ece_penalty, self.ice_opts.ece_min_len))
self.icep = None # IceAllPartials.
self.iceq = None # IceQuiver
self.icepq = None # IceQuiverPostprocess
self._nfl_splitted_fas = None
self.validate_inputs()
def validate_inputs(self):
"""
Validate input directories: root_dir, and
files: nfl_fa, bas_fofn, ccs_fofn.
"""
self.add_log("Validating inputs.")
errMsg = ""
if not op.exists(self.root_dir):
errMsg = "Root dir {d} is not an existing directory!".\
format(d=self.root_dir)
if not op.exists(self.nfl_fa):
errMsg = "Failed to find non-full-length reads {f}!".\
format(f=self.nfl_fa)
if self.bas_fofn is None:
errMsg = "bas_fofn (subreadset) must be specified."
if not op.exists(self.bas_fofn):
errMsg = "Failed to find bas fofn (subreadset) {f}!".format(
f=self.bas_fofn)
if errMsg != "":
self.add_log(errMsg, level=logging.ERROR)
raise ValueError(errMsg)
def run(self):
"""
First, split non-full-length (nfl) fasta files into smaller
chunks, assign nfl reads in each splitted fasta file
into unpolished isoform clusters and then merge all pickles
into self.nfl_all_pickle_fn.
Second, bin every 100 clusters, for each bin, call blasr,
samto5h, loadPulses, cmph5tools to create cmp.h5 files and
call quiver to polish each isoforms within each bin.
Finally, pick up good isoform clusters whose QV errors is less
than a threshold.
Save all high quality isoforms to hq_isoforms_fa|fq if they are not None
Save all low quality isoforms to lq_isoforms_fa|fq if they are not None
"""
if guess_file_format(self.bas_fofn) != FILE_FORMATS.BAM:
# Create input.fasta.fofn from bas_fofn
self.add_log("Creating fasta fofn from bas/bax.h5/bam fofn",
level=logging.INFO)
if self.fasta_fofn is None:
self.fasta_fofn = op.join(self.nfl_dir, "input.fasta.fofn")
self.add_log("fasta fofn={f}".format(f=self.fasta_fofn))
convert_fofn_to_fasta(fofn_filename=self.bas_fofn,
out_filename=self.fasta_fofn,
fasta_out_dir=self.nfl_dir)
else:
self.fasta_fofn = None
# Split non-full-length reads into smaller fasta files
# and save files to root_dir/nfl_00.fasta, ..., .
self.add_log("Splitting {nfl} into ".format(nfl=self.nfl_fa) +
"smaller files each containing {n} reads.".format(
n=self.ice_opts.nfl_reads_per_split),
level=logging.INFO)
self._nfl_splitted_fas = splitFasta(
input_fasta=self.nfl_fa,
reads_per_split=self.ice_opts.nfl_reads_per_split,
out_dir=self.nfl_dir,
out_prefix="input.split")
msg = "Splitted files are: " + "\n".join(self._nfl_splitted_fas)
self.add_log(msg, level=logging.INFO)
# Generating dazz DB for final.consensus.fasta
ref_obj = DazzIDHandler(input_filename=self.final_consensus_fa,
converted=False)
ref_obj.make_db()
msg = "Dazz DB made for: " + ref_obj.dazz_filename
self.add_log(msg, level=logging.INFO)
# Process nfl reads in each splitted fasta.
self.add_log("Initializing IceAllPartials.", level=logging.INFO)
self.icep = IceAllPartials(root_dir=self.root_dir,
fasta_filenames=self._nfl_splitted_fas,
ref_fasta=self.final_consensus_fa,
out_pickle=self.nfl_all_pickle_fn,
sge_opts=self.sge_opts,
ccs_fofn=self.ccs_fofn)
self.add_log("IceAllPartials log: {f}.".format(f=self.icep.log_fn),
level=logging.INFO)
self.icep.run()
self.add_log("IceAllPartials completed.", level=logging.INFO)
self.add_log("Initializing IceQuiver.", level=logging.INFO)
self.iceq = IceQuiver(root_dir=self.root_dir,
bas_fofn=self.bas_fofn,
fasta_fofn=self.fasta_fofn,
sge_opts=self.sge_opts,
tmp_dir=self.tmp_dir)
self.add_log("IceQuiver log: {f}.".format(f=self.iceq.log_fn),
level=logging.INFO)
self.iceq.run()
self.add_log("IceQuiver finished.", level=logging.INFO)
self.add_log("Initializing IceQuiverPostprocess.", level=logging.INFO)
self.icepq = IceQuiverPostprocess(root_dir=self.root_dir,
use_sge=self.sge_opts.use_sge,
quit_if_not_done=False,
ipq_opts=self.ipq_opts)
self.add_log(
"IceQuiverPostprocess log: {f}.".format(f=self.icepq.log_fn),
level=logging.INFO)
self.icepq.run()
self.add_log("IceQuiverPostprocess finished.", level=logging.INFO)
class Polish(IceFiles):
"""Polish isoforms clusters using Quiver."""
def __init__(self, root_dir, nfl_fa, bas_fofn, ccs_fofn,
ice_opts, sge_opts, ipq_opts, fasta_fofn=None,
tmp_dir=None):
"""
root_dir --- IceFiles.root_dir, usually data/clusterOutDir
nfl_fa --- non-full-length reads in fasta, e.g., isoseq_nfl.fasta
bas_fofn --- e.g. input.fofn of bas|bax.h5 files
ccs_fofn --- e.g. ccs.fofn of ccs files.
ipq_opts --- IceQuiverHQLQOptions
qv_trim_5: ignore QV of n bases in the 5' end
qv_trim_3: ignore QV of n bases in the 3' end
hq_quiver_min_accuracy: minimum allowed quiver accuracy
to mark an isoform as high quality
hq_isoforms_fa|fq: polished, hiqh quality consensus
isoforms in fasta|q
lq_isoforms_fa|fq: polished, low quality consensus
isoforms in fasta|q
"""
IceFiles.__init__(self, prog_name="IcePolish", root_dir=root_dir,
bas_fofn=bas_fofn, ccs_fofn=ccs_fofn,
fasta_fofn=fasta_fofn, tmp_dir=tmp_dir)
self.nfl_fa = realpath(nfl_fa)
self.ice_opts = ice_opts
self.sge_opts = sge_opts
self.ipq_opts = ipq_opts
self.add_log("ece_penalty: {0}, ece_min_len: {1}".format(self.ice_opts.ece_penalty, self.ice_opts.ece_min_len))
self.icep = None # IceAllPartials.
self.iceq = None # IceQuiver
self.icepq = None # IceQuiverPostprocess
self._nfl_splitted_fas = None
self.validate_inputs()
def validate_inputs(self):
"""
Validate input directories: root_dir, and
files: nfl_fa, bas_fofn, ccs_fofn.
"""
self.add_log("Validating inputs.")
errMsg = ""
if not op.exists(self.root_dir):
errMsg = "Root dir {d} is not an existing directory!".\
format(d=self.root_dir)
if not op.exists(self.nfl_fa):
errMsg = "Failed to find non-full-length reads {f}!".\
format(f=self.nfl_fa)
if self.bas_fofn is None:
errMsg = "bas_fofn (subreadset) must be specified."
if not op.exists(self.bas_fofn):
errMsg = "Failed to find bas fofn (subreadset) {f}!".format(f=self.bas_fofn)
if errMsg != "":
self.add_log(errMsg, level=logging.ERROR)
raise ValueError(errMsg)
def run(self):
"""
First, split non-full-length (nfl) fasta files into smaller
chunks, assign nfl reads in each splitted fasta file
into unpolished isoform clusters and then merge all pickles
into self.nfl_all_pickle_fn.
Second, bin every 100 clusters, for each bin, call blasr,
samto5h, loadPulses, cmph5tools to create cmp.h5 files and
call quiver to polish each isoforms within each bin.
Finally, pick up good isoform clusters whose QV errors is less
than a threshold.
Save all high quality isoforms to hq_isoforms_fa|fq if they are not None
Save all low quality isoforms to lq_isoforms_fa|fq if they are not None
"""
if guess_file_format(self.bas_fofn) != FILE_FORMATS.BAM:
# Create input.fasta.fofn from bas_fofn
self.add_log("Creating fasta fofn from bas/bax.h5/bam fofn",
level=logging.INFO)
if self.fasta_fofn is None:
self.fasta_fofn = op.join(self.nfl_dir, "input.fasta.fofn")
self.add_log("fasta fofn={f}".format(f=self.fasta_fofn))
convert_fofn_to_fasta(fofn_filename=self.bas_fofn,
out_filename=self.fasta_fofn,
fasta_out_dir=self.nfl_dir)
else:
self.fasta_fofn = None
# Split non-full-length reads into smaller fasta files
# and save files to root_dir/nfl_00.fasta, ..., .
self.add_log("Splitting {nfl} into ".format(nfl=self.nfl_fa) +
"smaller files each containing {n} reads.".format(
n=self.ice_opts.nfl_reads_per_split),
level=logging.INFO)
self._nfl_splitted_fas = splitFasta(input_fasta=self.nfl_fa,
reads_per_split=self.ice_opts.nfl_reads_per_split,
out_dir=self.nfl_dir,
out_prefix="input.split")
msg = "Splitted files are: " + "\n".join(self._nfl_splitted_fas)
self.add_log(msg, level=logging.INFO)
# Generating dazz DB for final.consensus.fasta
ref_obj = DazzIDHandler(input_filename=self.final_consensus_fa, converted=False)
ref_obj.make_db()
msg = "Dazz DB made for: " + ref_obj.dazz_filename
self.add_log(msg, level=logging.INFO)
# Process nfl reads in each splitted fasta.
self.add_log("Initializing IceAllPartials.", level=logging.INFO)
self.icep = IceAllPartials(
root_dir=self.root_dir,
fasta_filenames=self._nfl_splitted_fas,
ref_fasta=self.final_consensus_fa,
out_pickle=self.nfl_all_pickle_fn,
sge_opts=self.sge_opts,
ccs_fofn=self.ccs_fofn)
self.add_log("IceAllPartials log: {f}.".format(f=self.icep.log_fn),
level=logging.INFO)
self.icep.run()
self.add_log("IceAllPartials completed.", level=logging.INFO)
self.add_log("Initializing IceQuiver.", level=logging.INFO)
self.iceq = IceQuiver(root_dir=self.root_dir,
bas_fofn=self.bas_fofn,
fasta_fofn=self.fasta_fofn,
sge_opts=self.sge_opts,
tmp_dir=self.tmp_dir)
self.add_log("IceQuiver log: {f}.".format(f=self.iceq.log_fn),
level=logging.INFO)
self.iceq.run()
self.add_log("IceQuiver finished.", level=logging.INFO)
self.add_log("Initializing IceQuiverPostprocess.", level=logging.INFO)
self.icepq = IceQuiverPostprocess(root_dir=self.root_dir,
use_sge=self.sge_opts.use_sge,
quit_if_not_done=False,
ipq_opts=self.ipq_opts)
self.add_log("IceQuiverPostprocess log: {f}.".
format(f=self.icepq.log_fn), level=logging.INFO)
self.icepq.run()
self.add_log("IceQuiverPostprocess finished.", level=logging.INFO)