def run(self):
"""Assigning nfl reads to consensus isoforms and merge."""
# Call ice_partial.py to create a pickle for each splitted nfl fasta
self.createPickles()
# Wait for pickles to be created, if SGE is used.
self.waitForPickles(pickle_filenames=self.pickle_filenames,
done_filenames=self.done_filenames)
# Combine all pickles to a big pickle file: nfl_all_pickle_fn.
self.combinePickles(pickle_filenames=self.pickle_filenames,
out_pickle=self.nfl_all_pickle_fn)
# Create symbolic link if necessary
ln(self.nfl_all_pickle_fn, self.out_pickle)
# Close log
self.close_log()
def run(self):
"""Assigning nfl reads to consensus isoforms and merge."""
# Call ice_partial.py to create a pickle for each splitted nfl fasta
self.createPickles()
# Wait for pickles to be created, if SGE is used.
self.waitForPickles(pickle_filenames=self.pickle_filenames,
done_filenames=self.done_filenames)
# Combine all pickles to a big pickle file: nfl_all_pickle_fn.
self.combinePickles(pickle_filenames=self.pickle_filenames,
out_pickle=self.nfl_all_pickle_fn)
# Create symbolic link if necessary
ln(self.nfl_all_pickle_fn, self.out_pickle)
# Close log
self.close_log()
def run(self):
"""Check all quiver jobs are running, failed or done. Write high-quality
consensus and low-quality consensus to all_quivered.good|bad.fa|fq.
"""
job_stats = self.check_quiver_jobs_completion()
self.add_log("quiver job status: {s}".format(s=job_stats))
if self.use_sge is not True and job_stats != "DONE":
self.add_log("quiver jobs were not submitted via sge, " +
"however are still incomplete. Please check.",
level=logging.ERROR)
return -1
elif self.use_sge is True:
while job_stats != "DONE":
self.add_log("Sleeping for 180 seconds.")
sleep(180)
job_stats = self.check_quiver_jobs_completion()
if job_stats == "DONE":
break
elif job_stats == "FAILED":
self.add_log("There are some failed jobs. Please check.",
level=logging.ERROR)
return 1
elif job_stats == "RUNNING":
self.add_log("There are jobs still running, waiting...",
level=logging.INFO)
if self.quit_if_not_done is True:
return 0
else:
msg = "Unable to recognize job_stats {s}".format(job_stats)
self.add_log(msg, logging.ERROR)
raise ValueError(msg)
self.pickup_best_clusters(self.fq_filenames)
self.add_log("Creating polished high quality consensus isoforms.")
if self.hq_isoforms_fa is not None:
ln(self.quivered_good_fa, self.hq_isoforms_fa)
if self.hq_isoforms_fq is not None:
ln(self.quivered_good_fq, self.hq_isoforms_fq)
self.add_log("Creating polished low quality consensus isoforms.")
if self.lq_isoforms_fa is not None:
ln(self.quivered_bad_fa, self.lq_isoforms_fa)
if self.lq_isoforms_fq is not None:
ln(self.quivered_bad_fq, self.lq_isoforms_fq)
if self.summary_fn is not None:
self.write_summary(summary_fn=self.summary_fn,
isoforms_fa=self.final_consensus_fa,
hq_fa=self.hq_isoforms_fa,
lq_fa=self.lq_isoforms_fa)
self.close_log()
def run(self):
"""Check all quiver jobs are running, failed or done. Write high-quality
consensus and low-quality consensus to all_quivered.good|bad.fa|fq.
"""
job_stats = self.check_quiver_jobs_completion()
self.add_log("quiver job status: {s}".format(s=job_stats))
if self.use_sge is not True and job_stats != "DONE":
self.add_log("quiver jobs were not submitted via sge, " +
"however are still incomplete. Please check.",
level=logging.ERROR)
return -1
elif self.use_sge is True:
while job_stats != "DONE":
self.add_log("Sleeping for 180 seconds.")
sleep(180)
job_stats = self.check_quiver_jobs_completion()
if job_stats == "DONE":
break
elif job_stats == "FAILED":
self.add_log("There are some failed jobs. Please check.",
level=logging.ERROR)
return 1
elif job_stats == "RUNNING":
self.add_log("There are jobs still running, waiting...",
level=logging.INFO)
if self.quit_if_not_done is True:
return 0
else:
msg = "Unable to recognize job_stats {s}".format(job_stats)
self.add_log(msg, logging.ERROR)
raise ValueError(msg)
self.pickup_best_clusters(self.fq_filenames)
self.add_log("Creating polished high quality consensus isoforms.")
if self.hq_isoforms_fa is not None:
ln(self.quivered_good_fa, self.hq_isoforms_fa)
if self.hq_isoforms_fq is not None:
ln(self.quivered_good_fq, self.hq_isoforms_fq)
self.add_log("Creating polished low quality consensus isoforms.")
if self.lq_isoforms_fa is not None:
ln(self.quivered_bad_fa, self.lq_isoforms_fa)
if self.lq_isoforms_fq is not None:
ln(self.quivered_bad_fq, self.lq_isoforms_fq)
if self.summary_fn is not None:
self.write_summary(summary_fn=self.summary_fn,
isoforms_fa=self.final_consensus_fa,
hq_fa=self.hq_isoforms_fa,
lq_fa=self.lq_isoforms_fa)
self.close_log()
def runChimeraDetector(self):
"""Call chimera detection on full-length reads, and non-full-length
reads if required."""
# Create forward/reverse primers for chimera detection.
self._processPrimers(
primer_fn=self.primer_fn,
window_size=self.chimera_detection_opts.primer_search_window,
primer_out_fn=self.primer_chimera_fn,
revcmp_primers=True)
# Detect chimeras among full-length reads, separate flnc reads and
# flc reads.
logging.info("Detect chimeric reads from trimmed full-length reads.")
(self.summary.num_flnc, self.summary.num_flc,
self.summary.num_flnc_bases, _x) = \
self._detect_chimera(in_fasta=self._trimmed_fl_reads_fn,
out_nc_fasta=self.out_flnc_fn,
out_c_fasta=self.out_flc_fn,
primer_report_fn=self._primer_report_fl_fn,
out_dom=self.out_trimmed_fl_dom_fn,
num_reads=self.summary.num_fl,
job_name="fl")
assert(self.summary.num_fl == self.summary.num_flnc +
self.summary.num_flc)
logging.info("Done with chimera detection on trimmed full-length " +
"reads.")
# Detect chimeras among non-full-length reads if required, separate
# nflnc reads and nflc reads, rewrite self.primer_report_nfl_fn.
if self.chimera_detection_opts.detect_chimera_nfl is True:
logging.info("Detect chimeric reads from trimmed non-full-length " +
"reads.")
(self.summary.num_nflnc, self.summary.num_nflc, _x, _y) = \
self._detect_chimera(in_fasta=self._trimmed_nfl_reads_fn,
out_nc_fasta=self.out_nflnc_fn,
out_c_fasta=self.out_nflc_fn,
primer_report_fn=self._primer_report_nfl_fn,
out_dom=self.out_trimmed_nfl_dom_fn,
num_reads=self.summary.num_nfl,
job_name="nfl")
assert(self.summary.num_nfl == self.summary.num_nflnc +
self.summary.num_nflc)
logging.info("Done with chimera detection on trimmed " +
"non-full-length reads.")
# Concatenate out_nflnc_fn and out_nflc_fn as out_nfl_fn
cat_files(src=[self.out_nflnc_fn, self.out_nflc_fn],
dst=self.out_nfl_fn)
# Concatenate out_flnc and out_nflnc to make out_all_reads_fn
cat_files(src=[self.out_flnc_fn, self.out_nflnc_fn],
dst=self.out_all_reads_fn)
else:
# Soft link _trimmed_nfl_reads_fn as out_nfl_fn
ln(self._trimmed_nfl_reads_fn, self.out_nfl_fn)
# Concatenate out_flnc and out_nfl to make out_all_reads_fn
cat_files(src=[self.out_flnc_fn, self.out_nfl_fn],
dst=self.out_all_reads_fn)
# primer info of fl/nfl reads reported to _primer_report_fl_fn
# and _primer_report_nfl_fn, concatenate them in order to make
# a full report: primer_report_fn.
cat_files(src=[self._primer_report_fl_fn, self._primer_report_nfl_fn],
dst=self.primer_report_fn)
# Delete intermediate files.
self._cleanup([self._primer_report_nfl_fn,
self._primer_report_fl_fn])
def runChimeraDetector(self):
"""Call chimera detection on full-length reads, and non-full-length
reads if required."""
# Create forward/reverse primers for chimera detection.
self._processPrimers(
primer_fn_forward=self.primer_fn_forward,
primer_fn_reverse=self.primer_fn_reverse,
window_size=self.chimera_detection_opts.primer_search_window,
primer_out_fn=self.primer_chimera_fn,
revcmp_primers=True)
# Detect chimeras among full-length reads, separate flnc reads and
# flc reads.
logging.info("Detect chimeric reads from trimmed full-length reads.")
(self.summary.num_flnc, self.summary.num_flc,
self.summary.num_flnc_bases, _x) = \
self._detect_chimera(in_fasta=self._trimmed_fl_reads_fn,
out_nc_fasta=self.out_flnc_fn,
out_c_fasta=self.out_flc_fn,
primer_report_fn=self._primer_report_fl_fn,
out_dom=self.out_trimmed_fl_dom_fn,
num_reads=self.summary.num_fl,
job_name="fl")
assert(self.summary.num_fl == self.summary.num_flnc +
self.summary.num_flc)
logging.info("Done with chimera detection on trimmed full-length " +
"reads.")
# Detect chimeras among non-full-length reads if required, separate
# nflnc reads and nflc reads, rewrite self.primer_report_nfl_fn.
if self.chimera_detection_opts.detect_chimera_nfl is True:
logging.info("Detect chimeric reads from trimmed non-full-length " +
"reads.")
(self.summary.num_nflnc, self.summary.num_nflc, _x, _y) = \
self._detect_chimera(in_fasta=self._trimmed_nfl_reads_fn,
out_nc_fasta=self.out_nflnc_fn,
out_c_fasta=self.out_nflc_fn,
primer_report_fn=self._primer_report_nfl_fn,
out_dom=self.out_trimmed_nfl_dom_fn,
num_reads=self.summary.num_nfl,
job_name="nfl")
assert(self.summary.num_nfl == self.summary.num_nflnc +
self.summary.num_nflc)
logging.info("Done with chimera detection on trimmed " +
"non-full-length reads.")
# Concatenate out_nflnc_fn and out_nflc_fn as out_nfl_fn
cat_files(src=[self.out_nflnc_fn, self.out_nflc_fn],
dst=self.out_nfl_fn)
# Concatenate out_flnc and out_nflnc to make out_all_reads_fn
cat_files(src=[self.out_flnc_fn, self.out_nflnc_fn],
dst=self.out_all_reads_fn)
else:
# Soft link _trimmed_nfl_reads_fn as out_nfl_fn
ln(self._trimmed_nfl_reads_fn, self.out_nfl_fn)
# Concatenate out_flnc and out_nfl to make out_all_reads_fn
cat_files(src=[self.out_flnc_fn, self.out_nfl_fn],
dst=self.out_all_reads_fn)
# primer info of fl/nfl reads reported to _primer_report_fl_fn
# and _primer_report_nfl_fn, concatenate them in order to make
# a full report: primer_report_fn.
cat_files(src=[self._primer_report_fl_fn, self._primer_report_nfl_fn],
dst=self.primer_report_fn)
# Delete intermediate files.
self._cleanup([self._primer_report_nfl_fn,
self._primer_report_fl_fn])
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_fas = splitFasta(
input_fasta=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_fas), level=logging.INFO)
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)
# 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,
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,
fasta_filenames_to_add=self._flnc_splitted_fas[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,
fastq_filename=firstSplit_fq,
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
def run(self):
"""Call ICE to cluster consensus isoforms."""
self.add_log("Start to run cluster.", level=logging.INFO)
#self.ice_opts.flnc_reads_per_split=1000 #FOR DEBUGGING, REMOVE LATER
# 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_fas = splitFasta(
input_fasta=self.flnc_fa,
reads_per_split=self.ice_opts.flnc_reads_per_split,
out_dir=self.root_dir,
out_prefix="input.split")
self.add_log("Splitted files are: " +
"\n".join(self._flnc_splitted_fas),
level=logging.INFO)
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)
# Initialize cluster by clique
self.add_log("Finding maximal cliques: initializing IceInit.",
level=logging.INFO)
self.iceinit = IceInit(readsFa=firstSplit,
qver_get_func=self._probqv.get_smoothed,
ice_opts=self.ice_opts,
sge_opts=self.sge_opts)
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.icec = IceIterative(
fasta_filename=firstSplit,
fasta_filenames_to_add=self._flnc_splitted_fas[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,
fastq_filename=firstSplit_fq,
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)
# 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.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
def run(self):
"""Call ICE to cluster consensus isoforms."""
self.add_log("Start to run cluster.", level=logging.INFO)
# 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_fas = splitFasta(
input_fasta=self.flnc_fa,
reads_per_split=self.ice_opts.flnc_reads_per_split,
out_dir=self.root_dir,
out_prefix="input.split")
self.add_log("Splitted files are: " +
"\n".join(self._flnc_splitted_fas),
level=logging.INFO)
firstSplit = self._flnc_splitted_fas[0]
# Set up probabbility and quality value model
self._setProbQV(ccs_fofn=self.ccs_fofn, firstSplitFa=firstSplit)
# Initialize cluster by clique
# check if init.pickle already exists, if so, no need to run IceInit
if os.path.exists(self.initPickleFN):
self.add_log("{0} already exists. Reading to get uc.".format(self.initPickleFN), level=logging.INFO)
with open(self.initPickleFN) as f:
uc = cPickle.load(f)
else:
self.add_log("Finding maximal cliques.", level=logging.INFO)
self.iceinit = IceInit(readsFa=firstSplit,
qver_get_func=self._probqv.get_smoothed,
ice_opts=self.ice_opts,
sge_opts=self.sge_opts)
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("Iteratively clustering.", level=logging.INFO)
self.icec = IceIterative(
fasta_filename=firstSplit,
fasta_filenames_to_add=self._flnc_splitted_fas[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)
self.icec.run()
clean_up_after_ICE(self.root_dir)
# 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)
# Call quiver to polish predicted consensus isoforms.
if self.ice_opts.quiver is not True:
self.add_log("Creating a link to cluster report.")
ln(src=self.icec.report_fn, dst=self.report_fn)
self.add_log("Writing a summary to {f}".format(f=self.summary_fn),
level=logging.INFO)
self.writeSummary(fa=self.out_fa, summary_fn=self.summary_fn)
else: # self.ice_opts.quiver is True
#TODO review code
self.pol = Polish(root_dir=self.root_dir,
nfl_fa=self.nfl_fa,
bas_fofn=self.bas_fofn,
ccs_fofn=self.ccs_fofn,
hq_isoforms_fa=self.hq_isoforms_fa,
hq_isoforms_fq=self.hq_isoforms_fq,
lq_isoforms_fa=self.lq_isoforms_fa,
lq_isoforms_fq=self.lq_isoforms_fq,
ice_opts=self.ice_opts,
sge_opts=self.sge_opts)
self.pol.run()
# cluster report
self.add_log("Creating a link to cluster report.")
ln(src=self.pol.iceq.report_fn, dst=self.report_fn)
# Write a summary.
self.add_log("Writing a summary to {f}".format(f=self.summary_fn),
level=logging.INFO)
self.writeSummary(fa=self.out_fa, summary_fn=self.summary_fn,
hq_fa=self.pol.icepq.quivered_good_fa,
lq_fa=self.pol.icepq.quivered_bad_fa)
# Create log file.
self.close_log()
return 0
def run(self):
"""Call ICE to cluster consensus isoforms."""
self.add_log("Start to run cluster.", level=logging.INFO)
# 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_fas = splitFasta(
input_fasta=self.flnc_fa,
reads_per_split=self.ice_opts.flnc_reads_per_split,
out_dir=self.root_dir,
out_prefix="input.split")
self.add_log("Splitted files are: " +
"\n".join(self._flnc_splitted_fas),
level=logging.INFO)
firstSplit = self._flnc_splitted_fas[0]
# Set up probabbility and quality value model
self._setProbQV(ccs_fofn=self.ccs_fofn, firstSplitFa=firstSplit)
# Initialize cluster by clique
# check if init.pickle already exists, if so, no need to run IceInit
if os.path.exists(self.initPickleFN):
self.add_log("{0} already exists. Reading to get uc.".format(
self.initPickleFN),
level=logging.INFO)
with open(self.initPickleFN) as f:
uc = cPickle.load(f)
else:
self.add_log("Finding maximal cliques.", level=logging.INFO)
self.iceinit = IceInit(readsFa=firstSplit,
qver_get_func=self._probqv.get_smoothed,
ice_opts=self.ice_opts,
sge_opts=self.sge_opts)
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("Iteratively clustering.", level=logging.INFO)
self.icec = IceIterative(
fasta_filename=firstSplit,
fasta_filenames_to_add=self._flnc_splitted_fas[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)
self.icec.run()
clean_up_after_ICE(self.root_dir)
# 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)
# Call quiver to polish predicted consensus isoforms.
if self.ice_opts.quiver is not True:
self.add_log("Creating a link to cluster report.")
ln(src=self.icec.report_fn, dst=self.report_fn)
self.add_log("Writing a summary to {f}".format(f=self.summary_fn),
level=logging.INFO)
self.writeSummary(fa=self.out_fa, summary_fn=self.summary_fn)
else: # self.ice_opts.quiver is True
#TODO review code
self.pol = Polish(root_dir=self.root_dir,
nfl_fa=self.nfl_fa,
bas_fofn=self.bas_fofn,
ccs_fofn=self.ccs_fofn,
hq_isoforms_fa=self.hq_isoforms_fa,
hq_isoforms_fq=self.hq_isoforms_fq,
lq_isoforms_fa=self.lq_isoforms_fa,
lq_isoforms_fq=self.lq_isoforms_fq,
ice_opts=self.ice_opts,
sge_opts=self.sge_opts)
self.pol.run()
# cluster report
self.add_log("Creating a link to cluster report.")
ln(src=self.pol.iceq.report_fn, dst=self.report_fn)
# Write a summary.
self.add_log("Writing a summary to {f}".format(f=self.summary_fn),
level=logging.INFO)
self.writeSummary(fa=self.out_fa,
summary_fn=self.summary_fn,
hq_fa=self.pol.icepq.quivered_good_fa,
lq_fa=self.pol.icepq.quivered_bad_fa)
# Create log file.
self.close_log()
return 0