def run(self):
"""Call ICE to cluster consensus isoforms."""
self.add_log("Start to run cluster.", level=logging.INFO)
if self.ice_opts.targeted_isoseq:
first_split = 1000
self.ice_opts.flnc_reads_per_split = 10000
self.add_log("targeted_isoseq: further splitting JUST first split to 1000. Changing flnc_reads_per_split=10000.")
else:
first_split = None
# Split flnc_fa into smaller files and save files to _flnc_splitted_fas.
self.add_log("Splitting {flnc} into ".format(flnc=self.flnc_fa) +
"smaller files each containing {n} reads.".format(
n=self.ice_opts.flnc_reads_per_split),
level=logging.INFO)
self._flnc_splitted_fqs = splitFastq(
input_fastq=self.flnc_fa,
reads_per_split=self.ice_opts.flnc_reads_per_split,
out_dir=self.root_dir,
out_prefix="input.split",
first_split=first_split)
self.add_log("Splitted files are: " +
"\n".join(self._flnc_splitted_fqs),
level=logging.INFO)
firstSplit_fq = self._flnc_splitted_fqs[0]
firstSplit_fa = firstSplit_fq[:firstSplit_fq.rfind('.')] + '.fasta'
ice_fq2fa(firstSplit_fq, firstSplit_fa)
# -------- commenting out below because we already have FASTQ!
#firstSplit = self._flnc_splitted_fas[0]
#firstSplit_fq = firstSplit[:firstSplit.rfind('.')] + '.fastq'
#self.add_log("Converting first split file {0} + {1} into fastq\n".format(\
# firstSplit, self.ccs_fofn), level=logging.INFO)
## Convert this into FASTQ
#ice_fa2fq(firstSplit, self.ccs_fofn, firstSplit_fq)
#
## Set up probabbility and quality value model
#if self.ice_opts.use_finer_qv:
# self._setProbQV_ccs(self.ccs_fofn, firstSplit)
#else:
# self._setProbQV_fq(firstSplitFq=firstSplit_fq)
self._setProbQV_fq(firstSplitFq=firstSplit_fq)
# Initialize cluster by clique
if os.path.exists(self.initPickleFN):
self.add_log("Reading existing uc pickle: {0}".format(self.initPickleFN), level=logging.INFO)
with open(self.initPickleFN) as f:
uc = cPickle.load(f)
else:
self.add_log("Finding maximal cliques: initializing IceInit.",
level=logging.INFO)
self.iceinit = IceInit(readsFa=firstSplit_fa,
qver_get_func=self._probqv.get_smoothed,
ice_opts=self.ice_opts,
sge_opts=self.sge_opts,
qvmean_get_func=self._probqv.get_mean)
uc = self.iceinit.uc
# Dump uc to a file
self.add_log("Dumping initial clusters to {f}".format(
f=self.initPickleFN), level=logging.INFO)
with open(self.initPickleFN, 'w') as f:
cPickle.dump(uc, f)
# Run IceIterative.
self.add_log("Iterative clustering: initializing IceIterative.",
level=logging.INFO)
#self.add_log("In Cluster. DEBUG: Calling Cluster with {0} {1} {2} ".format(self.bas_fofn, self.ccs_fofn, self.fasta_fofn))
self.icec = IceIterative(
fasta_filename=firstSplit_fa,
fastq_filename=firstSplit_fq,
fastq_filenames_to_add=self._flnc_splitted_fqs[1:],
all_fasta_filename=self.flnc_fa,
ccs_fofn=self.ccs_fofn,
root_dir=self.root_dir,
ice_opts=self.ice_opts,
sge_opts=self.sge_opts,
uc=uc,
probQV=self._probqv,
use_ccs_qv=self.ice_opts.use_finer_qv)
self.add_log("IceIterative log: {f}.".format(f=self.icec.log_fn))
self.icec.run()
self.add_log("IceIterative completed.", level=logging.INFO)
# IceIterative done, write predicted (unplished) consensus isoforms
# to an output fasta
self.add_log("Creating a link to unpolished consensus isoforms.")
ln(self.icec.final_consensus_fa, self.out_fa)
#self.add_log("In Cluster. DEBUG: End Cluster with {0} {1} {2} ".format(self.bas_fofn, self.ccs_fofn, self.fasta_fofn))
# Call quiver to polish predicted consensus isoforms.
if self.ice_opts.quiver is not True:
self.add_log("Creating a link to cluster report.",
level=logging.INFO)
ln(src=self.icec.report_fn, dst=self.report_fn)
# Summarize cluster and write to summary_fn.
self.write_summary(summary_fn=self.summary_fn,
isoforms_fa=self.out_fa)
else: # self.ice_opts.quiver is True
self.add_log("Polishing clusters: initializing IcePolish.",
level=logging.INFO)
#self.add_log("In Cluster. DEBUG: Calling Polish with {0} {1} {2} ".format(self.bas_fofn, self.ccs_fofn, self.fasta_fofn))
self.pol = Polish(root_dir=self.root_dir,
nfl_fa=self.nfl_fa,
bas_fofn=self.bas_fofn,
ccs_fofn=self.ccs_fofn,
fasta_fofn=self.fasta_fofn,
ice_opts=self.ice_opts,
sge_opts=self.sge_opts,
ipq_opts=self.ipq_opts,
nfl_reads_per_split=self.nfl_reads_per_split)
self.add_log("IcePolish log: {f}.".format(f=self.pol.log_fn),
level=logging.INFO)
self.pol.run()
self.add_log("IcePolish completed.", level=logging.INFO)
# cluster report
self.add_log("Creating a link to cluster report.",
level=logging.INFO)
ln(src=self.pol.iceq.report_fn, dst=self.report_fn)
# Summarize cluster & polish and write to summary_fn.
self.write_summary(summary_fn=self.summary_fn,
isoforms_fa=self.out_fa,
hq_fa=self.pol.icepq.quivered_good_fa,
lq_fa=self.pol.icepq.quivered_bad_fa)
# Create log file.
self.close_log()
return 0
